R: Table nucleotides in whole BAM file(s)

nucStats {rbamtools} | R Documentation

## Table nucleotides in whole BAM file(s)

### Description

The function counts occurrence of the Nucleotides A,C,G,T for whole BAM file from `bamReader` object or a list of BAM files. Letters different from A,C,G,T are subsumed in the value N. The function returns a `data.frame` with 8 columns. The names indicate which position contains the count value each nucleotide. The function also calculates GC-content and AT/GC ratio which make up the last two columns. The returned data.frame contains one row for each reference sequence (when used for `bamReader`) or one row for each given BAM file name.

### Usage

    nucStats(object,...)

### Arguments

`object` | `bamReader` object. The reader must be opened and have initialized index.

`...` | Optional name for BAM-index files (argument name=idxInfiles).

### Value

data.frame

### Author(s)

Wolfgang Kaisers

### Examples

    bam<-system.file("extdata","accepted_hits.bam",package="rbamtools")
    nucStats(bam)
    idx<- system.file("extdata", "accepted_hits.bam.bai", package="rbamtools")
    nucStats(bam,idxInfiles=idx)
    reader<-bamReader(bam,idx=TRUE)
    nucStats(reader)
    range<-bamRange(reader,c(0,0,100000))
    nucStats(range)

[Package rbamtools version 2.16.17 Index]