bam2gr {PICS} | R Documentation |
Reads a bam file using Rsamtools
and extract the reads for each chromosome.
bam2gr(bamFile, chr=NULL, PE=FALSE, verbose=FALSE)
bamFile |
A character string, the name of the .bam file to read. |
chr |
An optional character string. If specified, only the selected chromosome will be returned. Speed up the computation. |
PE |
A |
verbose |
A |
Returns a GRanges
of all the reads for each chromosome.
The user might encounter a memory allocation error when using bam files of bigger sizes. Splitting the file by chromosome before calling bam2gr
will solve this issue.
For Paired-End data, non matched reads are discarded.
Renan Sauteraud