extract_encodepeaks: Extracts peaks from ENCODE data

In alice-szeliga/keles-pipeline: A Model to Predict Regulatory and Expression Modulating eQTLs

Description

extract_encode peaks takes ENCODE data and outputs a list of peaks with metadata, as well as lists of bed files and unique peaks.

Arguments

chipLocation:	string, file location of ENCODE ChIP metadata.tsv
dnaseLocation:	string, file location of ENCODE DNase metadata.tsv
dnamethLocation:	string, file location of ENCODE DNA methylation metadata.tsv
peakdir:	string, path of directory containing peak files in .bed format
outdir:	string, path of directory to save output

Value

NULL, but saves to disk an .Rda file of meta_peaks: a data.table of all the peak metadata bed.list.raw: a list of the raw bed file names bed.list.narrow1: a list of all the narrowpeak files uniquepeaks.raw: a list of the raw unique peaks uniquepeaks.narrow1: a list of the unique narrowpek files This is what is actually called by run_Encode.R

alice-szeliga/keles-pipeline documentation built on May 12, 2019, 5:35 a.m.