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 TSSs required at a given position (numeric) |
writeTable |
specifies whether the output should be written to a table. (logical) |
a matrix of tag counts (where the number of columns will equal the number of replicates in the sample) is appended to the data frame of the selected set of identified TSRs in the returned tssObject
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)