import_chrom: Read preprocessed genomic interaction files into an...

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

Description

Read preprocessed genomic interaction files into an InteractionSet object.

Usage

import_chrom(bed, raflist = NULL, workDir = getwd(), binned = FALSE)

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.
binned	Boolean, whether the matrix is already binned. Defaults to FALSE.

Value

An InteractionSet object containing all interactions from all input raf files, and the bin size (if any) in the metadata.

Examples

# You can import several specific raf files from the same directory
# (the working directory if no workDir is specified).
# myInteractions <- import_chrom(bed = "annotation.bed",
#                                raflist = list("1.raf", "2.raf"))

# Or just choose all raf files within a specific directory
myInteractions <- import_chrom(bed = "RFanno_HindIII.bed",
                               workDir = system.file("extdata", package = "chromium"),
                               binned = F)

AnnikaGable/chromium documentation built on May 5, 2019, 6:04 a.m.