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`. The name of the .bam file to read.
`chr` | A `character`. An optional character string. If specified, only the selected chromosome will be returned. Speed up the computation.
`PE` | A `logical`. Set to `TRUE` for paired-end sequencing data.
`verbose` | A `logical`. Print additional information about the data.

### Value

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.

### See Also

segmentPICS

[Package PICS version 2.34.0 Index]