getGapSites: Read 'gapSites'

In spliceSites: A bioconductor package for exploration of alignment gap positions from RNA-seq data

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

spliceSites documentation built on May 6, 2019, 3:05 a.m.