raer

Installation

if (!require("BiocManager",quietly=TRUE)) {    install.packages("BiocManager")}BiocManager::install("raer")

BiocManager::install("rnabioco/raer")

Quick start

library(raer)bam1fn<- raer_example("SRR5564269_Aligned.sortedByCoord.out.md.bam")bam2fn<- raer_example("SRR5564277_Aligned.sortedByCoord.out.md.bam")fafn<- raer_example("human.fasta")bams<- c("ko"=bam1fn,"wt"=bam2fn)rse<- pileup_sites(bams,fafn)

suppressMessages(library(SummarizedExperiment))rse#> class: RangedSummarizedExperiment#> dim: 1695 2#> metadata(0):#> assays(7): ALT nRef ... nC nG#> rownames(1695): site_SSR3_1_2 site_SSR3_2_2 ... site_DHFR_517_2#>   site_DHFR_518_2#> rowData names(4): REF rpbz vdb sor#> colnames(2): ko wt#> colData names(1): sampleassays(rse)#> List of length 7#> names(7): ALT nRef nAlt nA nT nC nGcolData(rse)#> DataFrame with 2 rows and 1 column#>         sample#>    <character>#> ko          ko#> wt          wt

assays(rse)$nRef[1:4, ]#>               ko wt#> site_SSR3_1_2 13 12#> site_SSR3_2_2 14 12#> site_SSR3_3_2 14 12#> site_SSR3_4_2 15 12assays(rse)$nAlt[1:4, ]#>               ko wt#> site_SSR3_1_2  0  0#> site_SSR3_2_2  0  0#> site_SSR3_3_2  0  0#> site_SSR3_4_2  0  0

fp<- FilterParam(only_keep_variants=TRUE,library_type="fr-first-strand",min_depth=2)rse<- pileup_sites(bams,fafn,param=fp)rse#> class: RangedSummarizedExperiment#> dim: 74 2#> metadata(0):#> assays(7): ALT nRef ... nC nG#> rownames(74): site_SSR3_102_2 site_SSR3_125_2 ... site_DHFR_430_2#>   site_DHFR_513_2#> rowData names(4): REF rpbz vdb sor#> colnames(2): ko wt#> colData names(1): sample

scbam_fn<- raer_example("5k_neuron_mouse_possort.bam")outdir<- tempdir()editing_sites<- GRanges(    c("2:579:-","2:625:-","2:589:-"    ),REF="A",ALT="G")cbs<- c("CACCAAACAACAACAA-1","TATTCCACACCCTCTA-1","GACCTTCAGTTGTAAG-1")sce<- pileup_cells(scbam_fn,sites=editing_sites,cell_barcodes=cbs,param=fp,output_directory=outdir)sce#> class: SingleCellExperiment#> dim: 3 3#> metadata(0):#> assays(2): nRef nAlt#> rownames(3): site_2_579_2_AG site_2_625_2_AG site_2_589_2_AG#> rowData names(2): REF ALT#> colnames(3): CACCAAACAACAACAA-1 TATTCCACACCCTCTA-1 GACCTTCAGTTGTAAG-1#> colData names(0):#> reducedDimNames(0):#> mainExpName: NULL#> altExpNames(0):

assays(sce)$nRef#> 3 x 3 sparse Matrix of class "dgCMatrix"#>                 CACCAAACAACAACAA-1 TATTCCACACCCTCTA-1 GACCTTCAGTTGTAAG-1#> site_2_579_2_AG                  0                  0                  1#> site_2_625_2_AG                  0                  0                  0#> site_2_589_2_AG                  1                  1                  2assays(sce)$nAlt#> 3 x 3 sparse Matrix of class "dgCMatrix"#>                 CACCAAACAACAACAA-1 TATTCCACACCCTCTA-1 GACCTTCAGTTGTAAG-1#> site_2_579_2_AG                  1                  1                  1#> site_2_625_2_AG                  1                  1                  1#> site_2_589_2_AG                  0                  0                  0

Related work