writeTSS {TSRchitect} | R Documentation

## writeTSS

### Description

`writeTSS` writes identified TSSs from a specified data set to a file in either tab or BED formats

### Usage

    writeTSS(experimentName, tssSetType, tssSet = 1, tssLabel = "TSS_",
      mixedorder = FALSE, fileType = "tab")

      ## S4 method for signature
    ## 'tssObject,character,numeric,character,logical,character'
    writeTSS(experimentName,
      tssSetType, tssSet = 1, tssLabel = "TSS_", mixedorder = FALSE,
      fileType = "tab")

### Arguments

`experimentName` | an S4 object of class tssObject containing information in slot @tssCountData
`tssSetType` | specifies the set to be written to file. Options are "replicates" or "merged". (character)
`tssSet` | number of the dataset to be processed (numeric).
`tssLabel` | specifies the label to be used in the name column of BED format output
`mixedorder` | a logical specifying whether the sequence names should be ordered alphanumerically ("10" following "9" rather than "1"). (logical)
`fileType` | the format of the file to be written. Possible choices are "tab" for tab-delimited output, "bed" for BED format, and "bedGraph" for for GFF3 format (character).

### Value

A table containing the specified TSS data set that is to be written to your working directory.

### Note

The .bed file written adheres to the standard six-column BED format, while "tab" format is identical to that of the data.frames containing TSS data.

For more information on the BED format, please visit https://genome.ucsc.edu/FAQ/FAQformat#format1

### Examples

    load(system.file("extdata", "tssObjectExample.RData", package="TSRchitect"))
    writeTSS(experimentName=tssObjectExample, tssSetType="replicates",
             tssSet=1, tssLabel="TSSsample1_", mixedorder=FALSE, fileType="tab")

[Package TSRchitect version 1.10.12 Index]