wig2CSARScore: Convert Data from a Wiggle Track (WIG) File to CSAR Binary...

In NarrowPeaks: Shape-based Analysis of Variation in ChIP-seq using Functional PCA

Description

Convert data from a wiggle track (WIG) file to CSAR binary format and extract read-enriched regions.

Usage

 wig2CSARScore(wigfilename, nbchr, chrle) 

Arguments

wigfilename	WIG file containing the enrichment-score signal of a transcription factor binding experiment.
nbchr	Number of chromosomes.
chrle	Vector of lengths of the chromosomes (in base pairs).

Details

The Wiggle format (WIG/bigWig) is described on the UCSC Genome Bioinformatics web site: http://genome.ucsc.edu/FAQ/FAQformat. It allows the display of continuous value data in the genome browser. Although specifically designed for post-processing of WIG files, resulting from the analysis of ChIP-seq experiments (with Bioconductor packages BayesPeak, CSAR, PICS, or other tools such as MACS, F-seq, etc.), NarrowPeaks can process other type of sequencing data encoded in WIG format in order to locate regions of high variability in the data.

Value

A list of two elements:

infoscores

A list with the same elements as reported by the function ChIPseqScore in the CSAR Bionductor package: chr (Chromosome names), chrL (Chromosome length (bp).), filenames (Name of the files where the score values are stored.), digits (Score values stored on the files need to be divided by 10^digits).

Author(s)

Pedro Madrigal, [e-mail]

References

Mateos JL, Madrigal P, et al. (2015) Combinatorial activities of SHORT VEGETATIVE PHASE and FLOWERING LOCUS C define distinct modes of flowering regulation in Arabidopsis. Genome Biology 16: 31.
Bailey T, Krajewski P, Ladunga I, Lefebvre C, Li Q, Liu T, Madrigal P, Taslim C, Zhang J (2013) Practical Guidelines for the Comprehensive Analysis of ChIP-seq data. PLOS Comput Biol. 9 (11): e1003326.
Muino JM, Kaufmann K, van Ham RC, Angenent GC, Krajewski P (2011) ChIP-seq analysis in R (CSAR): An R package for the statistical detection of protein-bound genomic regions. Plant Methods 7:11.

See Also

narrowpeaks, NarrowPeaks-package

Examples

owd <- setwd(tempdir())

##For this example we will use a subset of the AP1 ChIP-seq data (Kaufmann et
##al., 2010)
##The data is obtained after analysis using the CSAR package available in 
##Bioconductor 
data("NarrowPeaks-dataset")
writeLines(wigfile_test, con="wigfile.wig")

##Write binary files with the WIG signal values for each chromosome 
##independently and obtain regions of read-enrichment with score values greater
##than 't', allowing a gap of 'g'. Data correspond to enriched regions found up
##to 105Kb in the Arabidopsis thaliana genome
wigScores <- wig2CSARScore(wigfilename="wigfile.wig", nbchr = 1, 
chrle=c(30427671))

setwd(owd)

NarrowPeaks documentation built on April 28, 2020, 6:51 p.m.