procBam {casper} | R Documentation

## 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

### Details

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

### 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.

### Author(s)

Camille Stephan-Otto Attolini

### See Also

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

### Examples

    ##See example in calcExp

[Package casper version 2.14.0 Index]