createSignalTracks {metaseqR2} | R Documentation

## Create bigWig signal tracks

### 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 = "someone@example.com"),
            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")

[Package metaseqR2 version 1.2.0 Index]