processTSS {TSRchitect} | R Documentation

## processTSS

### Description

`processTSS` calulates the number of observed reads at a given TSS coordinate across an entire dataset.

### Usage

    processTSS(experimentName, n.cores, tssSet, writeTable)

    ## S4 method for signature 'tssObject,numeric,character,logical'
    processTSS(experimentName,
      n.cores = 1, tssSet = "all", writeTable = FALSE)

### Arguments

`experimentName` | an S4 object of class tssObject containing information in slot @tssTagData
`n.cores` | the number of cores to be used for this job. n.cores=1 means serial execution of function calls (numeric)
`tssSet` | default is "all"; to select a single tssSet, specify it (as character)
`writeTable` | specifies whether the output should be written to a file. (logical)

### Value

Creates a list of GenomicRanges containing TSS positions in slot tssTagData of the returned tssObject.

### Note

Note that the tssSet parameter must be of class character, even when selecting an individual dataset.

An example similar to the one provided can be found in the vignette (/inst/doc/TSRchitect.Rmd).

### Examples

    load(system.file("extdata", "tssObjectExample.RData",
    package="TSRchitect"))
    tssObjectExample <- processTSS(experimentName=tssObjectExample, n.cores=1,
    tssSet="all", writeTable=FALSE)

[Package TSRchitect version 1.8.9 Index]