procBam: Process BAM object
In casper: Characterization of Alternative Splicing based on Paired-End Reads

Description Usage Arguments Details Value Methods Author(s) See Also Examples

Process paired-end data stored in BAM object generated by scanBam. Outputs GRanges objects for reads and junctions.

1 2	procBam(bam, stranded=FALSE, seed=as.integer(1), verbose=FALSE, rname='null', keep.junx=FALSE, keep.flag=FALSE, ispaired=TRUE,...)

`bam`	BAM object generated by `scanBam`
`stranded`	Set to `TRUE` to indicate that the RNA-seq experiment preserved the strand information.
`seed`	Seed for random number generator
`verbose`	Set to `TRUE` to print progress information.
`rname`	Chromosome to process be combined with the `which` argument in the scanBam function
`keep.junx`	Option to store junction information. Only useful for finding denovo exons and transcripts.
`keep.flag`	Option to store aligment flag information.
`ispaired`	Set to `TRUE` is reads are paired.
`...`	Other arguments

In case of multihits with same start position for both reads but different insertions/deletions patterns only one alignment is chosen at random.

An object of class procBam containing reads with both ends correctly aligned and split according to the corresponding CIGAR. Unique identifiers by fragment are stored. Junctions spanned by reads are also stored in GRanges object if the argument \'keep.junx\' is set to TRUE.

signature(bam='list',stranded='logical',seed='integer',verbose='logical', rname='character',keep.junx='logical',keep.flag='logical'): Process paired-end data stored in BAM object generated by scanBam. Outputs GRanges objects for reads and (optionally) junctions.

Camille Stephan-Otto Attolini

scanBam from package Rsamtools, help("procBam-class"), getReads.