writeTSR-methods: *writeTSR*

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

Description

writeTSR writes identified TSRs from a specified data set to a file in selected format

Usage

writeTSR(
  experimentName,
  tsrSetType,
  tsrSet = 1,
  tsrLabel = "TSR_",
  mixedorder = FALSE,
  fileType = "tab"
)

## S4 method for signature 
## 'tssObject,character,numeric,character,logical,character'
writeTSR(
  experimentName,
  tsrSetType,
  tsrSet = 1,
  tsrLabel = "TSR_",
  mixedorder = FALSE,
  fileType = "tab"
)

Arguments

experimentName	an 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 (numeric).
tsrLabel	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, "bedGraph" for BedGraph format, and "gff" for for GFF3 format (character).

Value

A table containing the specified TSR 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 TSR 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"))
writeTSR(experimentName=tssObjectExample, tsrSetType="replicates",
         tsrSet=1, tsrLabel="TSRsample1_", mixedorder=FALSE, fileType="tab")

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