bam2gr: Pre-process bam files
In PICS: Probabilistic inference of ChIP-seq

Description Usage Arguments Value Note See Also

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

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

`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.

A GRanges of all the reads for each chromosome.

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.

segmentPICS

PICS documentation built on Nov. 8, 2020, 8:21 p.m.