guideAlignments: Read BAM file report, filter with valid PAM sequence, report...

In cancerdatasci/ceres: CERES for R

Description

Read BAM file report, filter with valid PAM sequence, report # of alignments

Usage

guideAlignments(bam.file, max.alns = 100, pam = "[ACGTN]GG|GG[ACGTN]",
  genome_id = "hg19", chromosomes = paste0("chr", c(as.character(1:22), "X",
  "Y")), include.no.align = F, as.df = T, guide_length = 20)

Arguments

bam.file	BAM file path
max.alns	only consider guides with fewer than this many alignments
pam	PAM sequence as regular expression
include.no.align	include guides that do not map to genome
as.df	return data.frame if TRUE, GRanges object if FALSE

Value

data.frame or GRanges object of results

cancerdatasci/ceres documentation built on May 20, 2019, 6:44 p.m.