In ramiromagno/wig: Import WIG Data into R in Long Format

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wig

The goal of {wig} is to import WIG data into R in long format.

Installation

Install {wig} from CRAN:

# Install from CRAN
install.packages("wig")

Or the current development version directly from GitHub:

# install.packages("remotes")
remotes::install_github("ramiromagno/wig")

Usage

To import a WIG file, simply use the function import_wig().

library(wig)
wig_file <- system.file("extdata", file = 'hg19-pik3ca.wig', package = "wig", mustWork = TRUE)

(wig_data <- import_wig(wig_file))

library(ggplot2)
ggplot(data = wig_data, mapping = aes(x = pos, y = val)) +
  geom_line(size = 0.1) +
  xlab('Chr 3 genomic position') +
  ylab('H3K4me3 raw counts')

The file hg19-pik3ca.wig is an example WIG file that contains H3K4me3 ChIP-Seq analysis of breast variant human mammary epithelial cell from RM035 (HS2615) using Illumina Genome Analyzer IIx. This WIG file has already been trimmed to a region where the gene PIK3CA can be found: chromosome 3, starting position 178,861,000 and ending position 178,894,000 (assembly hg19).

If you are interested, you can find more details about this sample in GEO: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM613874.

Admonition

The function import_wig() is to be used with smallish files, i.e., files whose genomic data comprises regions on the tens or few hundreds of kilobases.

If you really need to do serious work with WIG, bigWIG, or other type of genome annotation files, you are probably better off using packages from the R Bioconductor ecosystem, e.g. rtracklayer.

How to extract a region from a WIG file (outside of R)

If you have a WIG file that comprises a long genomic region, but you are only interested on a small genomic region, here are the steps to extract that region:

1. Download these two command-line tools: bigWigToWig and wigToBigWig from https://hgdownload.soe.ucsc.edu/admin/exe/linux.x86_64/. Navigate up one-level if your Operating System (OS) is not Linux and find the compiled tools for your OS.
2. Start by converting your WIG file to BigWIG with wigToBigWig:

wigToBigWig <my-not-so-small-wig-file>.wig.gz chromInfo.txt <a-Big-Wig-file>.bw

You are going to need a file with chromosome lengths. E.g., for assembly hg19 you can get chromInfo.txt.gz provided by UCSC from: ftp://hgdownload.cse.ucsc.edu/goldenPath/hg19/database/chromInfo.txt.gz.

1. Then, you can use bigWigToWig to select a specific region and convert back to WIG, e.g.:

bigWigToWig -chrom=chr3 -start=178861000 -end=178894000 <a-Big-WIG-file>.bw <my-small-wig-file>.wig

ramiromagno/wig documentation built on Nov. 22, 2022, 12:49 p.m.