addTagCountsToTSR {TSRchitect}R Documentation

addTagCountsToTSR

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 TSSs required at a given position (numeric)

writeTable

specifies whether the output should be written to a table. (logical)

Value

a matrix of tag counts (where the number of columns will equal the number of replicates in the sample) is appended to the data frame of the selected set of identified TSRs in the returned tssObject

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)


[Package TSRchitect version 1.8.9 Index]