ASEsetFromBam {AllelicImbalance} | R Documentation |
count alleles and create an ASEset direct from bam file instead of reading into R first.
ASEsetFromBam(gr, ...) ## S4 method for signature 'GRanges' ASEsetFromBam( gr, pathToDir, PE = TRUE, flagsMinusStrand = c(83, 163), flagsPlusStrand = c(99, 147), strandUnknown = FALSE, ... )
gr |
GenomicRanges of SNPs to create ASEset for |
... |
passed on to ASEsetFromBam function |
pathToDir |
Directory of bam files with index in same directory |
PE |
if paired end or not (default: TRUE) |
flagsMinusStrand |
flags that mark reads coming from minus strand |
flagsPlusStrand |
flags that mark reads coming from plus strand |
strandUnknown |
default: FALSE |
counts the alleles in a bam file based on GRanges positions.
Jesper R. Gadin
data(GRvariants) gr <- GRvariants ##no execution at the moment #pathToDir <- system.file('inst/extdata/ERP000101_subset', package='AllelicImbalance') #a <- ASEsetFromBam(gr, pathToDir)