rbamtools (version 2.4.0)

gapSiteList-class: Class "gapSiteList"

Description

The gapList class represents a list of Alignment gap (N-items in Cigar-data) sites . For each gap-site, left and right start and end positions as well as the gap-length are reported. Numbers of aligns supporting this site, number of left-sided start positions (

Objects from the Class

Objects can be created by calls of the form siteList(reader,coords)).

Examples

library(rbamtools)
bam<-system.file("extdata", "accepted_hits.bam", package="rbamtools")
idx<-paste(bam,"bai",sep=".")
# Open BAM file
reader<-bamReader(bam)
# Load BAM index file
load.index(reader,idx)
coords<-as.integer(c(0,0,249250621))
sl<-siteList(reader,coords)
size(sl)
nAligns(sl)
nGapAligns(sl)
sl
df<-as.data.frame(sl)
head(df)
bamClose(reader)