writeTSR {TSRchitect} | R Documentation |
writeTSR
writes identified TSRs
from a specified data set to a file in either tab or BED formats
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")
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, and "gff" for for GFF3 format (character). |
A table containing the specified TSR data set that is to be written to your working directory.
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
load(system.file("extdata", "tssObjectExample.RData", package="TSRchitect")) writeTSR(experimentName=tssObjectExample, tsrSetType="replicates", tsrSet=1, tsrLabel="TSRsample1_", mixedorder=FALSE, fileType="tab")