determineTSR {TSRchitect} | R Documentation

## determineTSR

### Description

`determineTSR` Identifies TSRs from entire TSS datasets as specified.

### Usage

    determineTSR(
      experimentName,
      n.cores,
      tssSetType,
      tssSet,
      tagCountThreshold,
      clustDist,
      ...
    )

    ## S4 method for signature
    ## 'tssObject,numeric,character,character,numeric,numeric'
    determineTSR(
      experimentName,
      n.cores = 1,
      tssSetType = c("replicates", "merged"),
      tssSet = "all",
      tagCountThreshold = 1,
      clustDist = 20,
      writeTable = FALSE,
      mixedorder = FALSE
    )

### Arguments

`experimentName` | an object of class tssObject containing information in slot @tssTagData
`n.cores` | the number of cores to be used for this job. ncores=1 means serial execution of function calls (numeric)
`tssSetType` | specifies the set to be clustered. Options are "replicates" or "merged". (character)
`tssSet` | default is "all"; if a single TSS dataset is desired, specify tssSet number (character)
`tagCountThreshold` | the number of TSSs required at a given position for it to be considered in TSR identification. (numeric)
`clustDist` | the maximum distance of TSSs between two TSRs in base pairs. (numeric)
`writeTable` | specifies whether the output should be written to a table. (logical)
`mixedorder` | a logical specifying whether the sequence names should be ordered alphanumerically in the output table ("10" following "9" rather than "1"). (logical)

### Value

creates a list of GenomicRanges-containing TSR positions in slot @tsrData of the returned tssObject object

### Note

An example similar to this one can be found in the vignette (/inst/doc/TSRchitect.Rmd)

### Examples

    load(system.file("extdata", "tssObjectExample.RData", package="TSRchitect"))
    tssObjectExample <- determineTSR(experimentName=tssObjectExample, n.cores=1,
    tssSetType="replicates", tssSet="1", tagCountThreshold=25, clustDist=20,
    writeTable=FALSE)

[Package TSRchitect version 1.16.0 Index]