analyze_tfs: Analyze TFs for a sample

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 the path to the directory with BED files for each TF, a BAM file with an aligned sequence and a TXT file with the normalized local coverage values for CNA, and estimates the corrected mean depth coverage values around TFBS, as well as the accessibilty scores for them. For better understanding check: https://www.nature.com/articles/s41467-019-12714-4

Usage

analyze_tfs(
  bin_path = "tools/bedtools2/bin/bedtools",
  bin_path2 = "tools/samtools/samtools",
  bed_dir = "",
  tfs = "",
  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_dir	Path to directory with BED files for TFBS
tfs	Number of TFs to analyze or a list with TFs to analyze. Default none will analyze all TFs in BED directory.
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 plots. Default TRUE.

Value

A DATA.FRAME with coverage data

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