add_chip_signals_to_sites: Adds ChIP-seq signals to the candidate sites

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

Adds ChIP-seq signals to the candidate sites

Description

Adds ChIP-seq signals to the candidate sites. It uses ChIP-seq signals (in BigWig format) from chip_signal_file. If chip_peak_file is not available, it will download the ChIP-seq signals from ENCODE database (using the sample ID provided in chip_signal_sampleID, and save to the directory chip_signal_dir).

Usage

add_chip_signals_to_sites(
  sites,
  chip_signal_file = NULL,
  chip_signal_sampleID = NULL,
  chip_signal_dir = "./",
  bigWigAverageOverBed_path = "bigWigAverageOverBed"
)

Arguments

sites	A data frame containing the candidate sites
chip_signal_file	ChIP-seq signal file (BigWig format).
chip_signal_sampleID	ENCODE sample ID of ChIP-seq signals (BigWig format).
chip_signal_dir	Directory to save the downloaded ChIP-seq signals.
bigWigAverageOverBed_path	Path to bigWigAverageOverBed executable.

Value

A data frame of candidate sites and ChIP-seq signals.

Examples

## Not run: 
sites_chip_signals - add_chip_signals_to_sites(sites, chip_signal_file='ChIPseq.signals.bigWig')

## End(Not run)

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