returns the bam data.frame with an additional column counts. Only relevant if the fasta file used for mapping input was previously collapsed via fastx_toolkit to return a fasta read name in the format of readnumber-totalcounts
Usage
getCountMatrix(bam_file,pseudo=FALSE)
Arguments
bam_file
An object of class DataFrame (from IRanges). Can be generated from readBam.
pseudo
Logical. If TRUE, assume the reads in the bam file does not have a count record and sets all counts to 1.
Value
An object of class data.frame having the values from the original bam file with an additional 'count' column.