addTagCountsToTSR-methods: *addTagCountsToTSR*

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

Description

addTagCountsToTSR adds a matrix of tag counts to a set of identified TSRs

Usage

addTagCountsToTSR(
  experimentName,
  tsrSetType,
  tsrSet = 1,
  tagCountThreshold = 1,
  writeTable = TRUE
)

## S4 method for signature 'tssObject,character,numeric,numeric,logical'
addTagCountsToTSR(
  experimentName,
  tsrSetType,
  tsrSet = 1,
  tagCountThreshold = 1,
  writeTable = TRUE
)

Arguments

experimentName	a S4 object of class tssObject containing information in slot @tssTagData
tsrSetType	specifies the set to be written to file. Options are "replicates" or "merged". (character)
tsrSet	number of the dataset to be processed, where 1 corresponds to the first slot, and so on. (numeric)
tagCountThreshold	number of tags required at a given TSS position in order to be included in the overall count for a TSR (numeric)
writeTable	specifies whether the output should be written to a table. (logical)

Value

a matrix of tag counts and median-normalized tag counts is appended to the data frame of the selected set of identified TSRs in the returned tssObject; note that the number of new columns is twice the number of replicates in the sample

Note

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 <- addTagCountsToTSR(experimentName=tssObjectExample,
tsrSetType="merged", tsrSet=1, tagCountThreshold=25, writeTable=FALSE)

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