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 BedGraph format (character). In case "bedGraph," three output files are produced: *_PLUS.bedGraph and *_MINUS.bedGraph, which record the number of TSS tags per position on plus and minus strand separately; and a combined *.bedGraph file which lists plus strand tag counts as positive numbers, minus strand tag counts as negative numbers, and positions with both plus and minus strand tag counts display the tag count corresponding to the highest absolute value.

### 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 1.18.0 Index]