rbamtools (version 2.0.1)

bamRange-class: Class "bamRange"

Description

bamRange represents a list of bamAlign objects which overlap with a defined region in a BAM-file.

Objects from the Class

Objects can be created by calls of the form range<-bamRange(reader, coords).

Examples

bam_file <- system.file("extdata", "accepted_hits.bam", package="rbamtools")
idx_file <- system.file("extdata", "accepted_hits.bam.bai", package="rbamtools")
reader<-bamReader(bam_file)
isOpen(reader)
align<-getNextAlign(reader)
loadIndex(reader,idx_file)
index.initialized(reader)
coords<-as.integer(c(0,0,1874))
range<-bamRange(reader,coords)
align<-getNextAlign(range)
bamClose(reader)