createSignalTracks: Create bigWig signal tracks

In metaseqR2: An R package for the analysis and result reporting of RNA-Seq data by combining multiple statistical algorithms

Description

This function creates bigWig files to be used for exploring RNA signal in genome browsers. When strands are separated, a UCSC genome browser trackhub is created to group tracks for the same sample. A link to the created data is returned.

Usage

    createSignalTracks(targets, org, urlBase = NULL, 
        stranded = FALSE, normTo = 1e+9, exportPath = ".",
        hubInfo = list(name = "MyHub", shortLabel = "My hub",
        longLabel = "My hub", email = "[e-mail]"),
        fasta = NULL, gtf = NULL, forceHub = FALSE, 
        overwrite = FALSE, rc = NULL)

Arguments

targets	a tab-delimited file with the experimental description or the output of readTargets. See also the sampleList argument in the main metaseqr2 pipeline.
org	See the org argument in the main metaseqr2 pipeline.
urlBase	a valid URL which is prepended to the created bigWig files.
stranded	Separate + and - strands and create separate bigWig files.
normTo	the total sum of signal to be used as the normalization target. See also the trackInfo argument in the main metaseqr2 pipeline.
exportPath	path to export tracks.
hubInfo	information regarding the track hub created when stranded=TRUE. See also the trackInfo argument in the main metaseqr2 pipeline.
overwrite	overwrite tracks if they exist? Defaults to FALSE.
fasta	reference genome in FASTA format for the case of analyzing a custom, non-directly supported organism. It will be converted to the .2bit format and written along with a track hub.
gtf	a GTF file describing gene models in the case of analyzing a custom, non-directly supported organism. It will be converted to the .bigBed format and written along with a track hub.
forceHub	when stranded=TRUE, a UCSC Genome Browser trackhub is created, otherwise only tracklines describing individual tracks. If TRUE, a trackhub is always created.
rc	Fraction of cores to use.

Value

A string with the link(s) to the created tracks.

Author(s)

Panagiotis Moulos

Examples

dataPath <- system.file("extdata",package="metaseqR2")
targets <- data.frame(samplename=c("C","T"),
    filename=file.path(dataPath,c("C.bam","T.bam")),  
    condition=c("Control","Treatment"),
    paired=c("single","single"),stranded=c("forward","forward"))
path <- tempdir()
write.table(targets,file=file.path(path,"targets.txt"),
    sep="\t",row.names=FALSE,quote=FALSE)
if (.Platform$OS.type == "unix")
    link <- createSignalTracks(file.path(path,"targets.txt"),"mm9")

metaseqR2 documentation built on Nov. 8, 2020, 7:34 p.m.