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 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)

[Package TSRchitect version 1.18.0 Index]