rbamtools (version 2.16.17)

countNucs: Counting nucleotides in bamAlign and bamRange

Description

The function counts occurrence of the Nucleotides A,C,G,T in bamAlign and bamRange objects. Any other values will be combined counted in the last value (N). The function returns an integer vector of length 5. The names indicate which position contains the count value each nucleotide.

Usage

countNucs(object)

Arguments

object

bamAlign or bamRange object.

Value

Integer (of length 4).

Examples

# NOT RUN {
# A) For bamAlign
align<-bamAlign("HWUSI-0001","ACCGGGTTTT","Qual/Strng","4M10N6M",refid=0,position=100)
countNucs(align)

# B) For bamRange
bam<-system.file("extdata","accepted_hits.bam",package="rbamtools")
reader<-bamReader(bam,idx=TRUE)
coords<-c(0,0,14730)
range<-bamRange(reader,coords)
countNucs(range)
# }