analyze_tfbs_around_position: Analyze Mean Coverage Depth around TFBS

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 a BED file with TFBS, a BAM file with an aligned sequence and a TXT file with the normalized local coverage values for CNA, and outputs the corrected mean depth coverage values around TFBS, as well as generates a PDF with a plot for them. For better understanding check: https://www.nature.com/articles/s41467-019-12714-4

Usage

analyze_tfbs_around_position(
  bin_path = "tools/bedtools2/bin/bedtools",
  bin_path2 = "tools/samtools/samtools",
  bed = "",
  bam = "",
  tfbs_start = 1000,
  tfbs_end = 1000,
  mean_cov = "",
  norm = "",
  threads = 1,
  cov_limit = 1000,
  max_regions = 1e+05,
  mapq = 0,
  verbose = FALSE,
  output_dir = "",
  plot = TRUE
)

Arguments

bin_path	Path to binary. Default tools/bedtools2/bin/bedtools
bin_path2	Path to secondary binary. Default tools/samtools/samtools
bed	Path to BED file.
bam	Path to BAM file.
tfbs_start	Number of bases to analyze forward from TFBS central point. Default 1000
tfbs_end	Number of bases to analyze backward from TFBS central point. Default 1000
mean_cov	Mean genome wide coverage. If not provided it will be estimated.
norm	Path to TXT file with normalized local coverage
threads	Number of threads. Default 1
cov_limit	Max base depth. Default 1000
max_regions	Max number of TFBS to analyze. Default 100000
mapq	Min quality of mapping reads. Default 0
verbose	Enables progress messages. Default FALSE
output_dir	Directory to output results. If not provided then outputs in current directory
plot	Create a plot with coverage data. Default TRUE.

Value

A DATA.FRAME with coverage data

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