bam2gr {PICS} | R Documentation

## pre-process bam files

### Description

Reads a bam file using `Rsamtools` and extract the reads for each chromosome.

### Usage

    bam2gr(bamFile, chr=NULL, PE=FALSE, verbose=FALSE)

### Arguments

`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 `logical`. This should be set to TRUE for paired-end sequencing data.
`verbose` | A `logical`. Print additional information about the data.

### Value

Returns a `GRanges` of all the reads for each chromosome.

### Note

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.

### Author(s)

Renan Sauteraud

### See Also

`segmentPICS`

[Package PICS version 2.26.0 Index]