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

In AnnikaGable/chromium: Analyze and visualize high throughput chromatin interaction data, such as Hi-C or ChIA-PET

Description

Read preprocessed genomic interaction files to produce RFanno and RFpairs.

Usage

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

# 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 May 5, 2019, 6:04 a.m.