addTagCountsToTSR {TSRchitect} | R Documentation |
addTagCountsToTSR
adds a matrix of tag counts to a set
of identified TSRs
addTagCountsToTSR( experimentName, tsrSetType, tsrSet = 1, tagCountThreshold = 1, writeTable = TRUE ) ## S4 method for signature 'tssObject,character,numeric,numeric,logical' addTagCountsToTSR( experimentName, tsrSetType, tsrSet = 1, tagCountThreshold = 1, writeTable = TRUE )
experimentName |
a 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, where 1 corresponds to the first slot, and so on. (numeric) |
tagCountThreshold |
number of tags required at a given TSS position in order to be included in the overall count for a TSR (numeric) |
writeTable |
specifies whether the output should be written to a table. (logical) |
a matrix of tag counts and median-normalized tag counts is appended to the data frame of the selected set of identified TSRs in the returned tssObject; note that the number of new columns is twice the number of replicates in the sample
An example similar to the one provided can be found in the vignette (/inst/doc/TSRchitect.Rmd)
load(system.file("extdata", "tssObjectExample.RData", package="TSRchitect")) tssObjectExample <- addTagCountsToTSR(experimentName=tssObjectExample, tsrSetType="merged", tsrSet=1, tagCountThreshold=25, writeTable=FALSE)