calculate_coverage_tfbs: Calculate 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 DATA.FRAME with TFBS positions, a BAM file with the sequence to analyze, a mean genome wide coverage, local coverage values for CNA, and outputs the corrected depth coverage values around TFBS and generates a TSS file with them. For better understanding check: https://www.nature.com/articles/s41467-019-12714-4

Usage

calculate_coverage_tfbs(
  bin_path = "tools/samtools/samtools",
  ref_data = "",
  bam = "",
  sample_name = "",
  tf_name = "",
  mean_cov = "",
  norm_log2 = "",
  tfbs_start = 1000,
  tfbs_end = 1000,
  cov_limit = 1000,
  mapq = 0,
  threads = 1,
  output_dir = ""
)

Arguments

bin_path	Path to binary. Default tools/samtools/samtools
ref_data	Data from BED file as Data.frame
bam	Path to BAM file.
sample_name	Sample name
tf_name	Transcription Factor name
mean_cov	Mean genome wide coverage.
norm_log2	Data.frame with normalized local coverage
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
cov_limit	Max base depth. Default 1000
mapq	Min quality of mapping reads. Default 0
threads	Number of threads. Default 1
output_dir	Directory to output results. If not provided then outputs in current directory
max_regions	Max number of TFBS to analyze. Default 100000

Value

A list of DATA.FRAME with the coverage per base of each TFBS

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