calculate_coverage_around_gp: Calculate Mean Coverage Depth around Genomic Position

In TearsWillFall/tfProfiling: An implementation of PeterUlz (https://github.com/PeterUlz/TranscriptionFactorProfiling) TranscriptionFactorProfiling pipeline in R for GNU/Unix based systems

Description

This function takes chromosome location, as well as strand information, and generates a coverage report around for it. This coverage can be normalized if local segmentation values for the region are given and further corrected by the the local coverage in the BAM

Usage

calculate_coverage_around_gp(
  bin_path = "tools/samtools/samtools",
  chr = "",
  position = "",
  strand = "",
  bam = "",
  norm_log2 = 1,
  start = 1000,
  end = 1000,
  mean_cov = 1,
  cov_limit = NA,
  mapq = 0
)

Arguments

bin_path	Path to binary. Default tools/samtools/samtools
chr	Chromosome
position	Genomic position within the chromosome
strand	Strand direction. If not available asumes + strand.
bam	Path to BAM file.
norm_log2	Local segment log2
start	Downstream distance from genomic position to estimate coverage
end	Upstream distance from genomic position to estimate coverage
mean_cov	Mean genome wide coverage.
cov_limit	Max coverage limit for position to be taken into account
mapq	Min quality of mapping reads. Default 0

Value

A DATA.FRAME with per base coverage por each genomic position

TearsWillFall/tfProfiling documentation built on Aug. 7, 2021, 9:40 a.m.