get_sites_counts: Extracts count matrices around candidate binding sites

In HarteminkLab/TOP: Predict transcription factor occupancy using DNase- or ATAC-seq data

Extracts count matrices around candidate binding sites

Description

Extracts counts around candidate binding sites on both strands from the genome counts data (BigWig files generated using count_genome_cuts()). It utilizes the extract bed function from the bwtool software to extract the read counts, then combines the counts into one matrix, with the first half of the columns representing the read counts on the forward strand, and the second half of the columns representing the read counts on the reverse strand.

Usage

get_sites_counts(
  sites,
  genomecount_dir,
  genomecount_name,
  tmpdir = genomecount_dir,
  bedGraphToBigWig_path = "bedGraphToBigWig",
  bwtool_path = "bwtool"
)

Arguments

sites	A data frame containing the candidate sites.
genomecount_dir	Directory for genome counts, the same as outdir in count_genome_cuts().
genomecount_name	File prefix for genome counts, the same as outname in count_genome_cuts().
tmpdir	Temporary directory to save intermediate files.
bedGraphToBigWig_path	Path to UCSC bedGraphToBigWig executable.
bwtool_path	Path to bwtool executable.

Value

A count matrix. The first half of the columns are the read counts on the forward strand, and the second half of the columns are the read counts on the reverse strand.

Examples

## Not run: 
# Extracts ATAC-seq count matrices around candidate sites
count_matrix <- get_sites_counts(sites,
                                 genomecount_dir='processed_data',
                                 genomecount_name='K562.ATAC')

## End(Not run)

HarteminkLab/TOP documentation built on July 27, 2023, 6:14 p.m.