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]