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A namedlist with r and LOD of markers within linkage groups.

Should output be written to a file? By defaultFALSE, ifTRUE then output,including plots fromMDSMap are saved in the same directory as the one used for input files. Theseplots are currently saved as pdf images. If a different plot format is required (e.g. for publications),then run theMDSMap functionestimate.map (or similar) directly and save the outputwith a different plotting function as wrapper around the map function call.

Directory to which map input files are initially written. Also used for output ifwrite_to_file=TRUE

prefix for the filenames of output plots.

Character string specifying the log filename to which standard output should be written.If NULL log is send to stdout.

Arguments passed toestimate.map.

An integer matrix with markers in rows and individuals in columns.

A list of character vectors specifying individual names that should be highlighted

Highlight colors. Vector of the same length ashighlight.

Character string specifying the log filename to which standard output should be written. If NULL log is send to stdout.

A linkage data.frame as output oflinkage.

Integer. The ploidy level of the species.

Numeric. The number of F1 individuals in the mapping population.

Logical. Plot the observed and expected relationship between r and LOD.

Numeric. Vector of upper and lower tolerances around expected line.

Character string. Specify which phase to examine for deviations (usually this is "coupling" phase).

A list of maps. Output of MDSMap_from_list.

A list of marker bins containing marker duplicates. One of the list outputs ofscreen_for_duplicate_markers

Optional argument to include the marker_assignments (output ofcheck_marker_assignment). If included, marker assignment information will also be copied.

Adata.frame as output oflinkage with arguments markertype1=c(1,0) and markertype2=NULL.

Adata.frame with markernames ("SxN_Marker"), linkage group ("LG") and homologue ("homologue")

A LOD score at which linkages between markers are significant.

Integer. The ploidy level of the plant species.

Integer. Number of chromosomes (linkage groups)

Character string specifying the log filename to which standard output should be written. If NULL log is send to stdout.

The markername

The assigned homologue

The assigned linkage group

A linkagedata.frame as output oflinkage.

Adata.frame with markernames ("SxN_Marker"), linkage group ("LG") and homologue ("homologue")

The name of the column in linkage_df harbouring the 1.0 markers

The name of the column in linkage_df harbouring the marker that are to be assigned.

The phase that is used to assign the markers (deprecated)

The number of chromosomes (linkage groups) in the species.

The LOD score at which a linkage to a linkage group is significant.

The ploidy of the plant species.

Logical. Should markers be assigned to homologues? IfFALSE markers will be assigned to all homologues

Character string specifying the log filename to which standard output should be written. If NULL log is send to stdout.

The assigned linkage group

The homologue with most linkages

Adata.frame with a column"marker" specifying markernames,and a column"cluster" specifying marker cluster

Optional. Acluster_stack for the other parent.Use this argument if cross-parent markers are used (e.g. when using 1.1 markers).

A linkagedata.frame as output oflinkage between bridge (e.g. 1.0 and 2.0) markers.

Optional. Alinkage_df specifying linkages between 1.0 and cross-parent markers in the other parent.Use this argument if cross-parent markers are used (e.g. when using 1.1, 2.1, 1.2 and/or 2.2 markers).The use of multiple types of cross-parent markers is allowed.

Integer. The LOD threshold specifying at which LOD score a link between 1.0 and bridging-type marker (e.g. 2.0) is used for clustering homologues.

Logical. Should clustering be executed without user input?

Integer. Expected number of chromosomes (linkage groups)

Name of the parent. Used in the main title of the plot.

The minimum number of links between a bridge marker and a cluster for that bridge to be considered. In the caseof a 2x0 marker for example, this argument means that the 2x0 marker must have at leastmin_links linkages of at least a LOD ofLOD_threshold withmarkers from each of the clusters involved, to be considered a single bridging link. Make this number higher if there are a lot of spurious links.

The minimum number of bridge markers needed to assign two homologues together as coming from the same chromosomal linkage group.See argumentmin_links for further details.

Logical, should only coupling linkages be used in the process? By defaultFALSE

Character string specifying the log filename to which standard output should be written. If NULL log is send to stdout.

The ploidy of parent 1 (must be even, 2 (diploid) or larger).

The ploidy of parent 2. If omitted (default=NULL) it isassumed to be equal to ploidy.

Can be either one of 'discrete' or 'probabilistic'. For the former (default), adosage_matrix must be supplied,while for the latter aprobgeno_df must be supplied.

An integer matrix with markers in rows and individuals in columns.

A data frame as read from the scores file produced by functionsaveMarkerModels of R packagefitPoly, or alternatively, a data frame containing the following columns:

SampleName

Name of the sample (individual)

MarkerName

Name of the marker

P0

Probabilities of dosage score '0'

P1...

Probabilities of dosage score '1' etc. (up to max dosage, e.g. P4 for tetraploid population)

maxP

Maximum genotype probability identified for a particular individual and marker combination

maxgeno

Most probable dosage for a particular individual and marker combination

geno

Most probable dosage for a particular individual and marker combination, ifmaxP exceeds a user-defined threshold (e.g. 0.9), otherwiseNA

character vector with the sample names of parent 1

character vector with the sample names of parent 2

character vector with the sample names of the F1 individuals

character vector with the sample names of any otherancestors or other samples of interest. The dosages of these samples willbe shown in the output (shifted if shiftParentsTRUE) but they are not usedin the selection of the segregation type.

ifTRUE at least all polysomic segtypes are considered;ifFALSE these are not specifically selected (but if e.g. disomic isTRUE,any polysomic segtypes that are also disomic will still be considered)

ifTRUE at least all disomic segtypes are considered (seepolysomic)

ifTRUE at least all mixed segtypes are considered (seepolysomic). A mixed segtype occurs when inheritance in one parent ispolysomic (random chromosome pairing) and in the other parent disomic (fullypreferential chromosome pairing)

The ploidy of parent 1 (must be even, 2 (diploid) or larger).

The ploidy of parent 2. If omitted it isassumed to be equal to ploidy.

the tab-separated text file to write the output to; if NA a temporary filecheckF1.tmp is created in the current working directory and deleted at end

NA or a numeric vector containing the weights of three qualitycriteria; do not need to sum to 1. If NA, the output will not contain acolumn qall_weights. Else the weights specify how qall_weights will becalculated from quality parameters q1, q2 and q3.

a minimum threshold value for the Pvalue of thebestParentfit segtype (with a smaller Pvalue the q1 quality parameter willbe set to 0)

a maximum threshold for the fracInvalid of thebestParentfit segtype (with a larger fraction of invalid dosages in the F1the q1 quality parameter will be set to 0)

a maximum threshold for the fraction of unscored F1samples (with a larger fraction of unscored samples in the F1the q3 quality parameter will be set to 0)

if specified, shiftmarkers must be a data frame withcolumns MarkerName and shift; for the markernames that match exactly(upper/lowercase etc) those in the input (eitherdosage_matrix orprobgeno_df), the dosages are increased by theamount specified in column shift,e.g. if shift is -1, dosages 2..ploidy are converted to 1..(ploidy-1)and dosage 0 is a combination of old dosages 0 and 1, for all samples.The segregation check is then performed with the shifted dosages.A shift=NA is allowed, these markers will not be shifted.The sets of markers in the input (eitherdosage_matrix orprobgeno_df) and shiftmarkersmay be different, but markers may occur only once in shiftmarkers.A column shift is added at the end of the returned data frame.
If parameter shiftParents isTRUE, the parental and ancestor scores areshifted as the F1 scores, ifFALSE they are not shifted.

TRUE if parents are scored in the same experimentand the samefitPoly run as the F1, elseFALSE.IfTRUE, their fraction missing scoresand conflicts tell something about the quality of the scoring. IfFALSE(e.g. when the F1 is triploid and the parents are diploid and tetraploid) thequality of the F1 scores can be independent of that of the parents.
If not specified,TRUE is assumed if ploidy2 == ploidy andFALSE ifploidy2 != ploidy

only used if parameter shiftmarkers is specified. IfTRUE,apply the shifts also to the parental and ancestor scores.By defaultTRUE ifparentsScoredWithF1 isTRUE

(defaultFALSE) ifTRUE, for each segtype 3 columnsare added to the returned data frame with the frqInvalid, Pvalue andmatchParents values for these segtype (see the description of the return value)

ifTRUE and parameter shiftmarkers is specified, _shf isappended to all marker names where shift is not 0. This is not required forany of the functions in this package but may prevent duplicated marker nameswhen using other software.

A namedlist with r and LOD of markers within linkage groups.

A list of maps. In the first column marker names and in the second their position.

The map function used in generating the maps, either one of "haldane" or "kosambi". By default "haldane" is assumed.

Numeric. Threshold for the LOD values to be displayed in heatmap, by default 5 (set at 0 to display all values)

Level of detail for heatmaps, by default 1 cM. Values less than 0.5 cM can have serious performance implications.

Option to specify graphical device for plotting, (either png or pdf), or by default "", in which case plots are directly plotted within R

Optional prefix appended to plot names if outputting plots.

A marker assignment matrix for parent 1 with markernames as rownames and at least containing the column"Assigned_LG"; the output ofhomologue_lg_assignment.

A marker assignment matrix for parent 2 with markernames as rownames and at least containing the column"Assigned_LG"; the output ofhomologue_lg_assignment.

Character string specifying the log filename to which standard output should be written. If NULL (by default) log is send to stdout.

Should messages be sent to stdout or log?

A data frame as read from the scores file produced by functionsaveMarkerModels of R packagefitPoly, or alternatively, a data frame containing the following columns:

SampleName

Name of the sample (individual)

MarkerName

Name of the marker

P0

Probabilities of dosage score '0'

P1...

Probabilities of dosage score '1' etc. (up to max dosage, e.g. P4 for tetraploid population)

maxP

Maximum genotype probability identified for a particular individual and marker combination

maxgeno

Most probable dosage for a particular individual and marker combination

geno

Most probable dosage for a particular individual and marker combination, ifmaxP exceeds a user-defined threshold (e.g. 0.9), otherwiseNA

A linkage data.frame as output oflinkage calculating linkage between 1.0 markers.

A numeric vector. Specifying a sequence of LOD thresholds at which clustering is performed.

Logical. Should the LOD of independence be used for clustering? (by default,FALSE.)

Expected number of chromosomes (linkage groups)

Ploidy level of the parent for which clustering is to be performed

Name of parent

Logical. Should a network be plotted. Recommended FALSE with large number of marker combinations.

Integer. The minimum cluster size to be returned. By default, a minimum cluster size of 1 is used, meaning allmarkers are returned. Setting this to a higher number can be useful for cleaning out mini-clusters that don't show strong linkageto the rest of the marker set.

Logical. Should exact cluster size be plotted as vertex labels?

Integer. The maximum vertex size. Only used ifplot_clust_size=FALSE.

Integer. The minimum vertex size. Only used ifplot_clust_size=FALSE.

Character string. By default all phases are used, but "coupling" or "repulsion" are also allowed.

Character string specifying the log filename to which standard output should be written. If NULL log is send to stdout (console).

Integer. Linkage group to investigate.

A data.frame as output oflinkage with argumentsmarkertype1 = c(1,0) andmarkertype2=NULL.

Adata.frame with columns"SxN_Marker" providing 1.0 markernames and"LG"and"homologue" providing linkage group and homologue respectively.

A numeric or vector of numerics giving LOD threshold(s) at which clustering should be performed.

Logical. ShouldLG_hom_stack be modified and returned?

Number of clusters in the output. If there are more clusters than this number only the nclust_out largest clusters are returned.

Network layout:"circular" or"stacked". If"n" no network is plotted.

Function of the graphics device to plot to (e.g.pdf,png,jpeg). The active device is used whenNULL

Offset of labels. Only used ifnetwork.layout="circular".

label character expansion. Only fornetwork.layout="circular".

Character string specifying the log filename to which standard output should be written. If NULL log is send to stdout.

Arguments passed todevice.

A list of maps. This is probably most conveniently built on-the-fly in the function call itself.If names are assigned to different maps (list items) these will appear abovethe maps. In cases of multiple comparisons, for example comparing 1 map of interest to 3 others, the map of interest canbe supplied multiple times in the list, interspersed between the other maps. See the example below for details.

The width in inches that linkage groups should be drawn. By default 0.2 inches is used.

The background colour of the maps, by default white. It can be useful to use a different background colour for the maps.In this case, supplybg.col as a vector of colour identifiers, with the same length asmaplist and corresponding to its elements in the same order. See the example below for details.

The colour with which links between maps are drawn, by default grey.

Option to thin the plotting of links between maps, which might be useful if there are very many shared markers in a small genetic region. By defaultNULL, otherwise supply a value (in cM) for the minimum genetic distance between linking-lines (e.g. 0.5).

Plot type, by default "karyotype". If "scatter" is requested a scatter plot is drawn, but only if the comparison is between 2 maps.

option to supply arguments to theplot function (e.g.main = to add a title to the plot)

A marker assignment file of the first parent. Should contain the number of linkages per LG per marker.

A marker assignment file of the second parent. Should be the same markertype as first parent and contain the number of linkages per LG per marker.

Number of linkage groups (chromosomes).

Ploidy level of plant species.

Filename of consensus output. No output is written if NULL.

Character string specifying the log filename to which standard output should be written. If NULL log is send to stdout.

A (modified) marker assignment matrix of the first parent.

A (modified) marker assignment matrix of the second parent.

Adata.frame with markernames, linkage group ("LG") and homologue ("homologue"), in which the linkage group numbers will be modified

A file with assigned markers of which (at least) part is present in both parents of the template parent.

A file with assigned markers of which (at least) part is present in both parents of the parent of which linkage group number are modified.

Logical, by defaultTRUE. IfFALSE, any discrepency in the number of linkage groups will not be merged, but removed instead.This can be needed if the number of chromosomes identified is not equal between parents, and the user wishes to proceed with a core set.

Character string specifying the log filename to which standard output should be written. If NULL log is send to stdout.

An integer matrix with markers in rows and individuals in columns.

ploidy level of the plant species. If parents have different ploidy level, ploidy of parent1.

ploidy level of the second parent. NULL if both parents have the same ploidy level.

Character string specifying the first (usually maternal) parentname.

Character string specifying the second (usually paternal) parentname.

Logical, by defaultFALSE. Should marker conversion information be returned? This output can be useful for later map phasing step,if original marker coding is desired (which is most likely the case).

Character string specifying the log filename to which standard output should be written. If NULL log is send to stdout.

An RADdata (S3 class) object; output of the functionPipelineMapping2Parents having followedthe prior steps needed in the polyRAD pipeline. See the polyRAD vignette for details.

An object of class multidog; output of the functionmultidog.

Output genotypes can be either "discrete" or "probabilistic", defaults to discrete.

If genotypes are being discretised, sets the minimum posterior probability in order to call a genotype with confidence. If maxpostprob < min_prob, that genotype is made missing. A default of 0.7 is suggested with no particular motivation.

data frame returned by function checkF1 when called withoutshiftmarkers

An integer matrix with markers in rows and individuals in columns.

character vector with names of the samples of parent 1

character vector with names of the samples of parent 2

ploidy of parents and F1 (correctDosages must not be used forF1 populations where the parents have a different ploidy, or where theparental genotypes are not scored together with the F1);same as used in the call to checkF1 that generated data.frame chk

if TRUE at least all polysomic segtypes are considered;if FALSE these are not specifically selected (but if e.g. disomic is TRUE,any polysomic segtypes that are also disomic will still be considered);same as used in the call to checkF1 that generated data.frame chk

if TRUE at least all disomic segtypes are considered (seeparam polysomic); same as used in the call to checkF1 that generateddata.frame chk

if TRUE at least all mixed segtypes are considered (seeparam polysomic). A mixed segtype occurs when inheritance in one parent ispolysomic (random chromosome pairing) and in the other parent disomic (fullypreferential chromosome pairing); same as used in the call to checkF1 thatgenerated data.frame chk

the threshold for the fraction of ALL samplesthat has the dosage that is assumed to be absent due to mis-fitting offitPoly; should be at least the assumed error rate of the fitPoly scoringassuming the fitted model is correct

A list of maps. In the first column marker names and in the second their position.

An integer matrix with markers in rows and individuals in columns. Either provide the unconverted dosages (i.e.before using theconvert_marker_dosages function), or converted dosages (i.e. screened data), in matrix form.The analysis and results are unaffected by this choice, but it may be simpler to understand the results if converted dosagesare used. Conversely, it may be advantageous to use the original unconverted dosages if particular marker alleles are beingtracked for (e.g.) the development of selectable markers afterwards.

Numeric. Size (in cM) of the bins to include. IfNULL (by default) then all markers are used (no binning).

Numeric vector. IfNULL (by default) then all positions are included, however if specified then outputis limited to a specific region, which is useful for later fine-mapping work.

Optional vector of marker names to remove from the maps. Default isNULL.

Output directory to which input files for TetraOrigin are written.

Character prefix to add to the .csv output filename.

Logical. Plot the marker positions of the selected markers usingplot_map.

Character string specifying the log filename to which standard output should be written. If NULL log is send to stdout.

Can be either one of 'discrete' or 'probabilistic'. For the former (default), at leastdosage_matrix.conv must be supplied,while for the latterchk must be supplied.

A list of maps. In the first column marker names and in the second their position.

Matrix of marker dosage scores with markers in rows and individuals in columns. Note that dosages must bein converted form, i.e. after having run theconvert_marker_dosages function. Errors may result otherwise.

Optional, by defaultNULL.The unconverted dosages (i.e. raw dosage data before usingtheconvert_marker_dosages function). Required iforiginal_coding isTRUE.

Probabilistic genotypes, for description see e.g.gp_overview. Required if probabilistic genotypes are used.

Output list as returned by functioncheckF1. Required if probabilistic genotypes are used.

Optional vector of marker names to remove from the maps. Default isNULL.

Logical. Should the phased map use the original marker coding or not? By defaultFALSE.

Number of significant linkages (as defined inhomologue_lg_assignment) required for high-confidence linkage group assignment.

Numeric. Lower bound for the rate at which homologue linkages (fraction of total for that marker) are recognised.

Integer. Ploidy of the organism.

Optional integer, by defaultNULL. Ploidy of parent 2, if different from parent 1.

A marker assignment matrix for parent 1 with markernames as rownames and at least containing the column"Assigned_LG".

A marker assignment matrix for parent 2 with markernames as rownames and at least containing the column"Assigned_LG".

character vector with names of the samples of parent 1

character vector with names of the samples of parent 2

One of the list elements (named 'marker_conversion_info') generated by the functionconvert_marker_dosages when the argumentmarker_conversion_infowas set toTRUE (not the default, so a user will typically have to re-run this step first).Required iforiginal_coding isTRUE.

Character string specifying the log filename to which standard output should be written. IfNULL log is send to stdout.

Logical, by defaultTRUE. Should details of the phasing process be given?

A list of cluster_stacks, the output ofcluster_SN_markers.

Integer. The LOD threshold specifying at which LOD score the markers divide into chromosomal groups

Integer. The LOD threshold specifying at which LOD score the markers divide into homologue groups

Integer. Expected number of chromosomes (linkage groups). Note that if this number of clusters are notpresent at LOD_chm, the function will abort.

Character string specifying the log filename to which standard output should be written. If NULL log is send to stdout.

Can be either one of 'discrete' or 'probabilistic'. For the former (default),dosage_matrix must be supplied,while for the latterprobgeno_df andchk must be supplied.

A marker assignment matrix with markernames as rownames and at least containing the column"Assigned_LG".

A named integer matrix with markers in rows and individuals in columns.

A data frame as read from the scores file produced by functionsaveMarkerModels of R packagefitPoly, or alternatively, a data frame containing the following columns:

SampleName

Name of the sample (individual)

MarkerName

Name of the marker

P0

Probabilities of dosage score '0'

P1...

Probabilities of dosage score '1' etc. (up to max dosage, e.g. P4 for tetraploid population)

maxP

Maximum genotype probability identified for a particular individual and marker combination

maxgeno

Most probable dosage for a particular individual and marker combination

geno

Most probable dosage for a particular individual and marker combination, ifmaxP exceeds a user-defined threshold (e.g. 0.9), otherwiseNA

Output list as returned by functioncheckF1. This argument is only needed if probabilistic genotypes are used.

A matrix with four columns specifying marker combinations to calculate linkage.IfNULL all combinations are used for which there are rf functions.Dosages of markers should be in the same order as specified in the names of rf functions.E.g. if using 1.0_2.0 and 1.0_3.0 types use:matrix(c(1,0,2,0,1,0,3,0), byrow = TRUE, ncol = 4)

Character string specifying the identifier of parent 1, by default "P1"

Character string specifying the identifier of parent 2, by default "P2"

Integer, either 1 or 2, with default 1, where 1 or 2 refers to parent1 or parent2 respectively.

Integer ploidy level of parent1, and also by default parent2. Argumentploidy2 can be used if parental ploidies differ.

Integer, by defaultNULL. If parental ploidies differ, use this to specify the ploidy of parent2.

Logical. Should markers that behave the same for both parents be converted to a workable format for that parent? E.g.: should 3.1 markers be converted to 1.3?

Type of pairing at meiosis, with options"random" or"preferential". By default, random pairing is assumned.

The estimates for preferential pairing parameters for parent 1 and 2, in range 0 <= p < 2/3. By default this is c(0,0) (so, no preferential pairing).See the functiontest_prefpairing and the vignette for more details.

Number of linkage groups (chromosomes).

Should messages be sent to stdout or log?

Character string specifying the log filename to which standard output should be written. If NULL log is send to stdout.

(Other) arguments passed tolinkage

Ploidy level

Type of pairing. Either "random" or "preferential".

Logical. Should nonavailable combinations be plotted with grey lines?

A data frame as read from the scores file produced by functionsaveMarkerModels of R packagefitPoly, or equivalently, a data frame containing the following columns:

SampleName

Name of the sample (individual)

MarkerName

Name of the marker

P0

Probabilities of dosage score '0'

P1...

Probabilities of dosage score '1' etc. (up to max dosage, e.g. P4 for tetraploid population)

maxP

Maximum genotype probability identified for a particular individual and marker combination

maxgeno

Most probable dosage for a particular individual and marker combination

geno

Most probable dosage for a particular individual and marker combination, ifmaxP exceeds a user-defined threshold (e.g. 0.9), otherwiseNA

a filtering threshold, by default 0.7, to identify individuals with more thanalpha non-missing (maximum) genotype probabilities falling below this cut-off. In other words, by using thisdefault settings (cutoff = 0.7 andalpha = 0.1), you require that 90in one of the possible genotype dosage classes. This can help identify problematic individuals with many examples of diffuse genotype calls. Lowering the threshold allows more diffuse calls to be accepted.

Option to specify the quantile of an individuals' scores that will be used to test againstcutoff, by default 0.1.

Can be either one of 'discrete' or 'probabilistic'. For the former (default),dosage_matrix must be supplied,while for the latterprobgeno_df andchk must be supplied.

An integer matrix with markers in rows and individuals in columns.

A data frame as read from the scores file produced by functionsaveMarkerModels of R packagefitPoly, or alternatively, a data frame containing the following columns:

SampleName

Name of the sample (individual)

MarkerName

Name of the marker

P0

Probabilities of dosage score '0'

P1...

Probabilities of dosage score '1' etc. (up to max dosage, e.g. P4 for tetraploid population)

maxP

Maximum genotype probability identified for a particular individual and marker combination

maxgeno

Most probable dosage for a particular individual and marker combination

geno

Most probable dosage for a particular individual and marker combination, ifmaxP exceeds a user-defined threshold (e.g. 0.9), otherwiseNA

Output list as returned by functioncheckF1. This argument is only needed if probabilistic genotypes are used.

List ofdata.frames with marker assignments for which the assignment analysis is already performed.

List of integer vectors of length 2. Specifying the markertypes in the same order as assigned_list.

A vector of function names to be used. If NULL all remaining linkage functions with SN markers are used.

Adata.frame with markernames ("SxN_Marker"), linkage group ("LG") and homologue ("homologue")

A character string specifying name of parent1.

A character string specifying the name of parent2.

Integer, either 1 or 2, with default 1, where 1 or 2 refers to parent1 or parent2 respectively.

Ploidy level of parent 1. If parent 2 has the same ploidy level, then also the ploidy level of parent 2.

Integer, by defaultNULL. If parental ploidies differ, use this to specify the ploidy of parent 2. Note that in cross-ploidy situations, ploidy2 must be smaller than ploidy.

Logical. Should markers that behave the same for both parents be converted to a workable format for that parent? E.g.: should 3.1 markers be converted to 1.3?

Type of pairing. Either"random" or"preferential". By default random pairing is assumed.

Expected number of chromosomes (linkage groups).

LOD threshold at which a linkage is considered significant.

Logical. Write intermediate linkage files to working directory?

Character string specifying the log filename to which standard output should be written. If NULL log is send to stdout.

Arguments passed tolinkage

An integer matrix with markers in rows and individuals in columns.

A vector of length 2 specifying the first markertype to compare. The first element specifies the dosage inwhich_parent (see below), the second in the other parent.

A vector of length 2 specifying the first markertype to compare. This argument is optional. If not specified, the function will calculatelinkage within the markertype as specified bymarkertype1.The first element specifies the dosage inwhich_parent (see below), the second in the other parent.

Character string specifying the name of parent1 as provided in the column-names of dosage_matrix. By default, "P1".

Character string specifying the other parent as provided in the column-names of dosage_matrix. By default, "P2".

Integer, either 1 or 2, with default 1, where 1 or 2 refers to parent1 or parent2 respectively. For example, if you wish to estimate linkage between markers with alleles that are polymorphic (i.e. segregating) and originates from parent1, then which_parent = 1. A bi-parental marker is a marker such as a 1x1 marker, so havinga segregating allele in both parents. For linkage estimation between pairs of bi-parental markers, the result does not depend on this argument. For linkage estimation between e.g. a1x0 and 1x1 marker, then which_parent should be 1. Similarly, to calculate linkage between 0x1 and 1x1 markers, which_parent should be 2.

Integer. The ploidy of the parent 1. If parent2 has the same ploidy level, then also the ploidy level of parent 2.

Integer, by defaultNULL. If parental ploidies differ, use this to specify the ploidy of parent2.

Apply a G2 test (LOD of independence) in addition to the LOD of linkage.

Logical. Should markers that behave the same for both parents be converted to a workable format for that parent? E.g.: should 3.1 markers be converted to 1.3? If unsure, set to TRUE.

Minimum LOD score of linkages to report. Recommended to use for large number (> millions) of marker comparisons in order to reduce memory usage.

Type of chromosomal pairing behaviour during meiosis, either"random" or"preferential". By default, random pairing is assumed (i.e. polysomic inheritance) is assumed. Note that this default does not affectlinkage estimation in a diploid, where pairing is arguably not random.

The estimates for preferential pairing parameters for the target and other parent, respectively, in range 0 <= p < 2/3. By default this is c(0,0) (so, no preferential pairing).See the functiontest_prefpairing and the vignette for more details.

Optional integer. Number of marker combinations per iteration.

A (very) conservative estimate of working memory in megabytes used per core. It only takes the size frequency matrices into account. Actual usage is more, especially with large number of linkages that are reported. Reduce memory usage by using a higher LOD_threshold.

Number of cores to use. Works both for Windows and UNIX (usingdoParallel). Useparallel::detectCores() to find out how many cores you have available.

Should messages be sent to stdout?

Logical, by defaultFALSE. IfTRUE, the complete output over all phases and showing marker combination counts is returned.

Character string specifying the log filename to which standard output should be written. If NULL log is send to stdout.

A data frame as read from the scores file produced by functionsaveMarkerModels of R packagefitPoly, or alternatively, a data frame containing the following columns:

SampleName

Name of the sample (individual)

MarkerName

Name of the marker

P0

Probabilities of dosage score '0'

P1...

Probabilities of dosage score '1' etc. (up to max dosage, e.g. P4 for tetraploid population)

maxP

Maximum genotype probability identified for a particular individual and marker combination

maxgeno

Most probable dosage for a particular individual and marker combination

geno

Most probable dosage for a particular individual and marker combination, ifmaxP exceeds a user-defined threshold (e.g. 0.9), otherwiseNA

Output list as returned by functioncheckF1

Option to include the most likely (discrete) parental dosage scores, used mainly for internal calls of this function. By defaultNULL

A vector of length 2 specifying the first markertype to compare. The first element specifies the dosage intarget_parent (and the second in the other parent).

A vector of length 2 specifying the first markertype to compare. This argument is optional. If not specified, the function will calculatelinkage within the markertype as specified bymarkertype1.The first element specifies the dosage intarget_parent (and the second in the other parent).

Which parent is being targeted (only acceptable options are "P1" or "P2"), ie. which parent is of specific interest? If this is the maternal parent, please specify as "P1". If the paternal parent, please use "P2". The actual identifiers of the two parents areentered using the argumentsparent1_replicates andparent2_replicates.

Apply a G2 test (LOD of independence) in addition to the LOD of linkage.

Minimum LOD score of linkages to report. Recommended to use for large number (> millions) of marker comparisons in order to reduce memory usage.

The estimates for preferential pairing parameters for parent 1 and 2, in range 0 <= p < 2/3. By default this is c(0,0) (so, no preferential pairing).See the functiontest_prefpairing and the vignette for more details.

Optional integer. Number of marker combinations per iteration.

A (very) conservative estimate of working memory in megabytes used per core. It only takes the size frequency matrices into account. Actual usage is more, especially with large number of linkages that are reported. Reduce memory usage by using a higher LOD_threshold.

Number of cores to use. Works both for Windows and UNIX (usingdoParallel). Useparallel::detectCores() to find out how many cores you have available.

Should messages be sent to stdout?

Check theqall_mult column ofchk, and filter out markers withqall_mult = 0. By defaultFALSE.

Either"approx" or"mappoly". If"approx" (the default method), then an approximated estimator is used which introducesa small amount of bias in the estimator of recombination frequency. If method"mappoly" is specified, the full likelihood is used in theestimation, leading to an unbiased estimator (this has been implemented in the mappoly package of Marcelo Mollinari). Themappoly method hashigher computational demands which may introduce problems for larger datasets, but will lead to higher accuracy overall.

Character string specifying the log filename to which standard output should be written. If NULL log is send to stdout.

A dosagematrix.

A linkagedata.frame.

Numeric. Threshold at which markers are binned. Is calculated if NA.

Numeric. Threshold at which markers are binned. Is calculated if NA.

A character string specifying the name of the target parent.

A character string specifying the name of the other parent.

The maximum number of markers per homologue. If specified, LOD threshold is optimized based on this number.

Maximum number of iterations to find optimum LOD threshold. Only used ifmax_marker_nr is specified.

Character string specifying the log filename to which standard output should be written. If NULL log is send to stdout.

A linkage data.frame with binned markers removed.

A data.frame containing binned markers and their representatives.

Integer. Number markers left.

An integer matrix with markers in rows and individuals in columns.

Integer. Ploidy of parent 1, and .

Ploidy of parent 2, by defaultNULL, as it is assumed ploidy2 equals ploidy.

Type of pairing. "random" or "preferential".

Column name of first parent. Usually maternal parent.

Column name of second parent. Usually paternal parent.

The relative number of incompatible dosages per genotype that results in reportingthis genotype as incompatible. Incompatible dosages are greater than maximum number of alleles than can be inherited orsmaller than the minimum number of alleles that can be inherited.

Logical, by defaultTRUE - should intermediate messages be written to stout?

Logical, by defaultFALSE. Returns only a shortened output with parental dosage summary, used internally by some functions.

Character string specifying the log filename to which standard output should be written. IfNULL log is send to stdout.

frequency table of different markertypes. Names start with parentnames, and behind that the dosage score.

Rate of incompatible ("impossible") marker scores (given as percentages of the total number of observed marker scores per marker class)

progeny names having incompatible dosage scores higher than threshold at progeny_incompat_cutoff.

Adata.frame with markernames, linkage group ("LG") and homologue ("homologue")

The ploidy level of the plant species.

The linkage group where the to be merged homologue fragments are in.

A list of vectors of length 2, specifying the numbers of the homologue fragments to be merged. User input is asked ifNULL.

Character string specifying the log filename to which standard output should be written. If NULL log is send to stdout.

A data.frame as output oflinkage with arguments markertype1=c(1,0) and markertype2=NULL.

A data.frame with a column "SxN_Marker" specifying markernames,a column "homologue" specifying homologue cluster and "LG" specifying linkage group.

Integer. Linkage group number of interest.

Numeric. LOD threshold of linkages which are plotted.

Maximum y-limit of the plots.

Character string specifying the log filename to which standard output should be written. If NULL log is send to stdout.

A frequency table of the different classes of dosages in the progeny. The column names start with"n_". Followed by the dosage of the first marker and then of the second.

Preferential pairing parameter for parent 1, numeric value in range 0 <= p1 < 2/3

Preferential pairing parameter for parent 2, numeric value in range 0 <= p2 < 2/3

Number of cores to use for parallel processing (deprecated).

A matrix with recombination frequencies for the different phases

A matrix with LOD scores for the different phases

A matrix with log likelihood ratios for the different phases

A character string specifying the phasing strategy."MLL" for maximum likelihood en"MINR" for minimum recombination frequency.

The phases between markers that are possible. Same order and length as column names of output matrices.

An integer matrix with markers in rows and individuals in columns.

Character string specifying the first (usually maternal) parentname.

Character string specifying the second (usually paternal) parentname.

Character string specifying the log filename to which standard output should be written. If NULL log is send to stdout.

Arguments passed tobarplot

A linkage data.frame as output oflinkage calculating linkage between 1.0 markers.

A list of cluster_stacks, the output ofcluster_SN_markers.

Integer. The LOD threshold specifying at which LOD score the markers divide into chromosomal groups

Expected number of chromosomes (linkage groups)

Logical. Should the LOD of independence be used for clustering? (by default,FALSE.)

Character string specifying the log filename to which standard output should be written. If NULL log is send to stdout (console).

A dataframe of a map that defines a linkage group.

A list of maps were each item represents a homoloogue.

A list of maps. In the first column marker names and in the second their position.

A list of the same length of maplist with vectors of length 2 that specifies thelimits in cM from and to which the plotted chromosomes should be highlighted.

The background colour of the map.

The color of the highlight. Only used ifhighlight is specified.

Optional. The column name of the value to be plotted as marker color.

Optional. The column name of the value to be plotted beside the markers.

Color palette used to plot values. Only used if colnames of the values are specified.

Logical. Should the markers be coloured by type? If TRUE, dosage_matrix should be specified.

Optional (by defaultNULL). Dosage matrix of marker genotypes, input oflinkage

Character string specifying the first (usually maternal) parentname.

Character string specifying the second (usually paternal) parentname.

Logical. Should a legend be drawn?

Arguments passed toplot

Optional extra arguments to pass tolegend, by default a list with x = 1 and y = 120 (position of the legend). Additional arguments should be passed using name = value, i.e. as a named list. Note that argumentslty (= 1) andlwd (= 2) havealready been used internally (as well aslegend andcol), so cannot be re-specified without causing an error.

A list of phased linkage maps, the output ofcreate_phased_maplist

Integer. Ploidy of the organism.

Optional integer, by defaultNULL. Ploidy of parent 2, if different from parent 1.

Vector of colours for the integrated, parent1 and parent2 maps, respectively.

Width of the linkage maps, by default 0.2

Optional vector of titles for maps, by default names of maplist, or titles LG1, LG2 etc. are used.

A frequency table of the different classes of dosages in the progeny. The column names start with"n_". Followed by the dosage of the first marker and then of the second.

Number of cores to use for parallel processing (deprecated).

A matrix with recombination frequencies for the different phases

A matrix with LOD scores for the different phases

A matrix with log likelihood ratios for the different phases

A character string specifying the phasing strategy."MLL" for maximum likelihood en"MINR" for minimum recombination frequency.

The phases between markers that are possible. Same order and length as column names of output matrices.

A frequency table of the different classes of dosages in the progeny. The column names start with"n_". Followed by the dosage of the first marker and then of the second.

Number of cores to use for parallel processing (deprecated).

A matrix with recombination frequencies for the different phases

A matrix with LOD scores for the different phases

A matrix with log likelihood ratios for the different phases

A character string specifying the phasing strategy."MLL" for maximum likelihood en"MINR" for minimum recombination frequency.

The phases between markers that are possible. Same order and length as column names of output matrices.

A frequency table of the different classes of dosages in the progeny. The column names start with"n_". Followed by the dosage of the first marker and then of the second.

Number of cores to use for parallel processing (deprecated).

A matrix with recombination frequencies for the different phases

A matrix with LOD scores for the different phases

A matrix with log likelihood ratios for the different phases

A character string specifying the phasing strategy."MLL" for maximum likelihood en"MINR" for minimum recombination frequency.

The phases between markers that are possible. Same order and length as column names of output matrices.

A frequency table of the different classes of dosages in the progeny. The column names start with"n_". Followed by the dosage of the first marker and then of the second.

A matrix with recombination frequencies for the different phases

A matrix with LOD scores for the different phases

A matrix with log likelihood ratios for the different phases

A character string specifying the phasing strategy."MLL" for maximum likelihood en"MINR" for minimum recombination frequency.

The phases between markers that are possible. Same order and length as column names of output matrices.

A linkage data.frame as output oflinkage.

A character string specifying the main title

Integer specifying chromosome

Maximum r value to plot

IfTRUE (by default), an attempt is made to reduce the plot density using hexagonal binning from theggplot2 package. This is recommended for large datasets, where the number of pairwise estimates becomes high.

The number of bins in each direction, passed to ggplot2::geom_hex. Only used iftidyplot = TRUE. Increasing this numbercan lead to slower but more accurate plotting.

An integer matrix with markers in rows and individuals in columns.

An integer at which margin the missing value frequency will be calculated. A value of 1 means rows (markers), 2 means columns (individuals)

Missing value frequency cut off. At this frequency, rows or columns are removed from the dataset. If NULL user input will be asked after plotting the missing value frequency histogram.

A character vector of length 2, specifying the parent names.

Logical. Should the percentage of markers removed as breakdown per markertype be plotted? Can only be used if margin = 1.

Character string specifying the log filename to which standard output should be written. If NULL log is send to stdout.

Logical. Should removed instances be printed?

An integer matrix with markers in rows and individuals in columns.

Correlation coefficient cut off. At this correlation coefficient, individuals are merged. If NULL user input will be asked after plotting.

Logical. Should correlation coefficients be plotted? Can be memory/CPU intensive with high number of individuals.

Character string specifying the log filename to which standard output should be written. If NULL log is send to stdout.

A data frame as read from the scores file produced by functionsaveMarkerModels of R packagefitPoly, or alternatively, a data frame containing the following columns:

SampleName

Name of the sample (individual)

MarkerName

Name of the marker

P0

Probabilities of dosage score '0'

P1...

Probabilities of dosage score '1' etc. (up to max dosage, e.g. P4 for tetraploid population)

maxP

Maximum genotype probability identified for a particular individual and marker combination

maxgeno

Most probable dosage for a particular individual and marker combination

geno

Most probable dosage for a particular individual and marker combination, ifmaxP exceeds a user-defined threshold (e.g. 0.9), otherwiseNA

The ploidy of parent 1

character vector with the sample names of parent 1

character vector with the sample names of parent 2

character vector with the sample names of the F1 individuals

Correlation coefficient cut off to declare duplicates. At this correlation coefficient, individuals are merged. IfNULL user input will be asked after plotting.

Logical. Should correlation coefficients be plotted? Can be memory/CPU intensive with high number of individuals.

Character string specifying the log filename to which standard output should be written. IfNULL log is send to stdout.

An integer matrix with markers in rows and individuals in columns.

Logical. Should missing values be imputed if non-NA in duplicated marker? By default,TRUE.IfFALSE the dosage scores of representing marker are represented in the filtered_dosage_matrix.

Logical. Should an informative plot about duplicate cluster size be given? By default,TRUE.

Ploidy level of parent 1. Only needed ifestimate_bin_size isTRUE

Integer, by defaultNULL. If parental ploidies differ, use this to specify the ploidy of parent 2. Only needed ifestimate_bin_size isTRUE

Expected number of chromosomes (linkage groups). Only needed ifestimate_bin_size isTRUE

Logical, by defaultFALSE. IfTRUE, a very rudimentary calculation is made to estimatethe average size of a marker bin, assuming a uniform distribution of cross-over events and on average one cross-over per bivalent.

Character string specifying the log filename to which standard output should be written. If NULL log is send to stdout.

An integer matrix with markers in rows and individuals in columns.

A list of integrated chromosomal maps, as generated by e.g.MDSMap_from_list. In the first column marker names and in the second their position.

Adata.frame with markernames ("SxN_Marker"), linkage group ("LG") and homologue ("homologue"),the output ofdefine_LG_structure orbridgeHomologues usually.

Character string specifying the parent to be tested for preferential pairing as provided in the columnnames of dosage_matrix, by default "P1".

The other parent, by default "P2"

The ploidy level of the species, by default 4 (tetraploid) is assumed.

The smallest distance to be considered a true distance on the linkage map, by default distances less than 0.5 cM are considered essentially zero.

Method to correct p values of Binomial test for multiple testing, by default the FDR correction is used, other options are available, inherited fromp.adjust

Should messages be sent to stdout? IfNULL log is send to stdout.

Phased maps in list format, the output ofcreate_phased_maplist

Directory to which TetraploidSNPMap files are written, by default written to "TetraploidSNPMap_QTLfiles" folder

Character string of filename stem to write the output files to, by default "TSNPM" with linkage groups names appended

The ploidy of the species, currently only 4 is supported by TetraploidSNPMap

Should messages be sent to stdout?

A list of maps. In the first column marker names and in the second their position. All map data arecompiled into a single MapChart file.

Directory to which .mct files are written, by default the same directoryas forMDSMap_from_list

A character string added to the first lines of the .mct file, by default a datestamp is recorded.

Character string of filename to write the .mct file to, by default "MapFile"

To how many decimal places should marker positions be specified (default = 2)?

Logical, by defaultFALSE, ifTRUE, the marker names will be diplayed in theMapChart output as well.

A linkagedata.frame.

A character string specifying a file open for writing.

A character string added to the first lines of the .pwd file.

Character string specifying the log filename to which standard output should be written. If NULL log is send to stdout.

A nested list.

Character string. Directory name to which to write the structure.

Logical. Save as R object?

Character. Prefix of R object. Only used ifsave_as_object = TRUE.

Character. File extension. Default is ".txt".

Arguments passed towrite.table

A nestedlist with linkage group on the first level and homologue on the second.

A character string specifying the name of the target parent.

Logical. Are the markers binned? This information is used in the pwd header.

A character string specifying the directory in which the files are written. Defaults to working directory.

Character string specifying the log filename to which standard output should be written. If NULL log is send to stdout.