tallyWrapper: A wrapper for catching mismatch nucleotides

In TapscottLab/SeqPipelineTools: Pipeline tools for RNA-seq or ChIP-seq data

Usage

tallyWrapper(bamFiles, genome = "hg38", destination = ".", cores = 1L)

Arguments

bamFiles
genome
destination
cores

See Also

See Also as catchMismatch

Examples

## Not run: 
cores <- 4L
mainDir <- "/fh/fast/tapscott_s/CompBio/RNA-Seq/hg38.dsRNA"
bamDir <- "/fh/fast/tapscott_s/CompBio/RNA-Seq/Sean/MB135_dsRNA/hg38_bwa"
bamFiles <- list.files(bamDir, full.name=TRUE, pattern=".bam$")[2:5]
source("/fh/fast/tapscott_s/CompBio/R_package/SeqPipelineTools/R/mismatchTools.R"
)

tally <- tallyWrapper(bamFiles, destination=file.path(mainDir, "test"),
                      cores=cores)
lapply(tally, SeqPipelineTools:::freqAIMismatch, exclude.SNP=TRUE)

## End(Not run)

TapscottLab/SeqPipelineTools documentation built on May 16, 2019, 2:28 a.m.