GenVisR (version 1.0.4)

compIdent_bamRcnt: Count nucleotide reads at SNP locations

Description

Given the bam file path, count the number of reads at specified snp locations

Usage

compIdent_bamRcnt(bamfile, genome, target = NULL, debug = FALSE)

Arguments

bamfile

Path to the bam file

genome

Object of class BSgenome corresponding to a genome of interest

target

Object of class data frame containing target locations in 1-base format and containing columns "chr", "start", "end", "var", "name"

debug

Boolean specifying if test datasets should be used for debugging.

Value

object of class data frame containing readcount information