casper (version 2.6.0)

procBam: Process BAM object

Description

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

Usage

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

Arguments

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

Value

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.

Methods

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.

Details

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

See Also

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

Examples

##See example in calcExp