Adds ChIP-seq signals to the candidate sites — add_chip_signals_to

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).

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

if (FALSE) {
sites_chip_signals - add_chip_signals_to_sites(sites, chip_signal_file='ChIPseq.signals.bigWig')
}