prcTSS: _prcTSS()_

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

Description

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

Usage

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.

BrendelGroup/TSRchitect documentation built on March 3, 2021, 1:45 a.m.