read_bed_raf: Read preprocessed genomic interaction files to produce RFanno...

Description Usage Arguments Value Examples

View source: R/import_and_subset.R

Description

Read preprocessed genomic interaction files to produce RFanno and RFpairs.

Usage

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read_bed_raf(bed, raflist = NULL, workDir = getwd())

Arguments

bed

File name of a bed file without header, with columns for chromosome (Ensembl format, no "chr"), start, end, and restriction fragment ID of each restriction fragment.

raflist

A list of file names containing the interactions. The files are in raf format, meaning they contain two columns (no header) with the interacting restriction fragment IDs. If raflist=NULL, all raf files in the directory will be read.

workDir

The directory where all input files are located. Defaults to the current working directory.

Value

A list consisting of an RFanno dataframe containing the restriction fragment annotation, and an RFpairs dataframe containing the interacting restriction fragment pairs.

Examples

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# RFanno <- read_bed_raf(bed = "annotation.bed", raflist = list("1.raf", "2.raf"))[[1]]
# RFpairs <- read_bed_raf(bed = "annotation.bed", raflist = list("1.raf", "2.raf"))[[2]]

AnnikaGable/chromium documentation built on July 12, 2018, 4 p.m.