Movatterモバイル変換

bakR 1.0.1

Updated Stan array syntax to be compatible with current rstanversion
Hack to address Hmisc binning edge case (seehttps://github.com/harrelfe/Hmisc/issues/169).

Functions for visualizing (VisualizeDropout),quantifying (QuantifyDropout), and correcting(CorrectDropout) metabolic label-induced dropout of RNAduring library preparation have been added.
New simulation function (simulate_relative_bakRData)which better captures the relative nature of RNA-seq and can accuratelysimulate dropout.
New experimental function (DissectMechanism) fordetermining how likely that any observed differential expression isdriven by transcriptional or post-transcriptional regulation.DissectMechanism is a rewrite and extension of thepreviously developedNSSHeat2 function, which itself was animprovement of the now deprecatedNSSHeat.
Can now provide fraction new estimates (e.g., from a tool likeGRAND-SLAM) as input to bakR. GRAND-SLAM input functionality is furthersupported by the newGSprocess function that willfacilitate converting from GRAND-SLAM output to bakR input.
FnPCA has been deprecated in favor ofFnPCA2 which accepts input differently and fixes somebugs.
Read count filtering now includes two filters. One read count thatall samples must pass, and one that only all replicates in a singleExp_ID need to pass. This facilitates identifying large increases ordecreaes in expression.
Several new vignettes to discuss much of the new functionalitydiscussed above.
Several small bug fixes

Small edit to configuration files that address compilation issuesthat can arise on some systems. Deals with “file too big” errors” duringpackage installation from source.

Implemented long read sequencing data analysis strategy. RunbakRFit() with Long = TRUE to use k-means clustering (k = 2) formutation rate and fraction new estimation. Need to have Ckmeans.1d.dppackage installed to do this (not installed during bakRinstallation).

Fixed bug in reliableFeatures. high_p was supposed to be the maximumallowable mutation rate (# of mutations/# of Ts) in reads from -s4Ucontrols, but was instead the maximum allowable average number of T-to-Cmutations in reads from these controls.

Fixed bug in cBprocess that didn’t properly check that features ofinterest provided by the FOI argument were valid.

Added QC_check(), a function to perform quality control analysiswith bakRFit objects. Looks for any problems in your data that willimpair bakR’s performance, generates a number of diagnosticvisualizations, and makes suggestions about what to do next.
Fixed plot coloring bug in plotMA() and plotVolcano().
Fixed bug that led to problems when the number of -s4U replicates> +s4U replicates in one or more Exp_IDs
Implemented improved U-content adjustment for MCMC implementation.Also impacts accuracy of StanRateEst = TRUE mutation rate estimationstrategy.
Increased default number of features to use for StanRateEst mutationrate estimation strategy.
Improved scaling of NSSHeat() output matrix columns.
Created a new function NSSHeat2() that implements a differentmechanism scoring function than NSSHeat().