writeTSS-methods: *writeTSS*

In BrendelGroup/TSRchitect: Promoter identification from large-scale TSS profiling data

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")

BrendelGroup/TSRchitect documentation built on March 3, 2021, 1:45 a.m.