processTSS-methods: *processTSS*

In TSRchitect: Promoter identification from large-scale TSS profiling data

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)

TSRchitect documentation built on Nov. 8, 2020, 8:11 p.m.