prcTSS: _prcTSS()_

Description Usage Arguments Value

Description

An internal function, invoked via processTSS, that creates an expression matrix for all TSSs within a given TSS experiment (in slot tssTagData)

Usage

1
prcTSS(experimentName, n.cores, tssSet, writeTable)

Arguments

experimentName

- a S4 object of class tssObject containing information in slot tssTagData

n.cores

the number of cores to be used for this job.

tssSet

- number of the dataset to be analyzed

writeTable

- if set to TRUE, writes a data frame containing the TSSs positions and their abundance to your workspace

Value

prcTSS fills the slot experimentName@tssCountData[[tssSet]] in the tssObject experimentName with a matrix of unique TSS positions (rows) and observed tag counts in each position for data set tssSet; precisely, each entry of the matrix consists of "seq" (chr), "TSS" (num), "nTAGs" (num), and "strand" (+ or -), corresponding to the sequence identifier, position, tag count, and strand, respectively.


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