getGapSites {spliceSites} | R Documentation

## Read `gapSites`

### Description

`getGapSites` and `alignGapList` read gap-site data from single BAM-files (given as `bamReader`) and return a `gapSites` object. `getGapSites` reads data for one seqid (given as 1-based numeric value). `alignGapList` reads the whole BAM-file. The functions test for opened reader and initialized index.

### Usage

    getGapSites(reader,seqid,startid=1)

### Arguments

`reader` | bamReader (rbamtools). An opened instance of `bamReader` with initialized index.
`seqid` | Numeric. 1-based index of reference sequence for which gap-sites are to be read.
`startid` | Numeric. Default: 1. Determines start value for `id` column from which the values are ascending ennumerated. `startid` greater than 1 allow to produce unique values over multiple BAM-files.

### Details

`getGapSites` internally calls `rbamtools::gapList`. `alignGapList` internally calls `rbamtools::bamGapList`. 'nProbes' values are set to 1.

### Value

gapSites

### Author(s)

Wolfgang Kaisers

### Examples

    bam<-system.file("extdata", "rna_fem.bam", package="spliceSites")
    reader<-bamReader(bam,idx=TRUE)
    gal<-getGapSites(reader,1,startid=10)
    gal
    gal<-alignGapList(reader)
    gal

[Package spliceSites version 1.28.0 Index]