MakeBiasCorrectionTableBAM: Generate n-mer bias tables from a given bam file

In sojbaek/bagfootr: Bi-vAriate Genomic Footprinting (BaGFoot)

Description

This function generate n-mer bias tables from a given BAM file. If the mappability files directory is given, mappability is used to generate the bias table. The Reference genome must be given to run this function.

Usage

MakeBiasCorrectionTableBAM(
  bamfile = "",
  outfile = "",
  refgenome = "",
  np = 6,
  mapdir = "",
  atac = F
)

Arguments

bamfile	Path to the input bam file
outfile	Output Filename
refgenome	Reference genome, eg) "mm9", "hg19"
np	Number of base pairs, 2 = dimer, 4 = tetramer, 6 = hexamer (default)
mapdir	Directory to the mappability files
atac	Logical, T for ATAC-seq data

Value

Output Filename

sojbaek/bagfootr documentation built on Aug. 22, 2020, 9:44 p.m.