add_chip_peak_labels_to_sites: Adds ChIP-seq peak labels to the candidate sites

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

Adds ChIP-seq peak labels to the candidate sites

Description

Adds ChIP-seq peak labels to the candidate sites. It uses ChIP-seq peaks from chip_peak_file if available. If chip_peak_file is not available, it will download the ChIP-seq peaks from ENCODE database (using the sample ID provided in chip_peak_sampleID, and save to the directory chip_peak_dir).

Usage

add_chip_peak_labels_to_sites(
  sites,
  chip_peak_file = NULL,
  chip_peak_sampleID = NULL,
  chip_peak_dir = "./"
)

Arguments

sites	A data frame containing the candidate sites
chip_peak_file	ChIP-seq peak file (.bed.gz format)
chip_peak_sampleID	ENCODE sample ID of ChIP-seq peaks (.bed.gz format)
chip_peak_dir	Directory to save the downloaded ChIP-seq peaks

Value

A data frame of candidate sites and binary ChIP-seq peak labels (bound: 1, unbound: 0).

Examples

## Not run: 
sites_chip_labels <- add_chip_peak_labels_to_sites(sites, chip_peak_file='ChIPseq.peaks.bed.gz')

## End(Not run)

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