addAnnotationToTSR {TSRchitect} | R Documentation |
addAnnotationToTSR
associates an identified promoter
with a given gene, if found upstream and on the same strand within
a specified range.
addAnnotationToTSR(experimentName, tsrSetType, tsrSet = 1, upstreamDist, downstreamDist, feature, featureColumnID, writeTable = TRUE) ## S4 method for signature ## 'tssObject, ## character, ## numeric, ## numeric, ## numeric, ## character, ## character, ## logical' addAnnotationToTSR(experimentName, tsrSetType, tsrSet = 1, upstreamDist = 1000, downstreamDist = 200, feature = "gene", featureColumnID = "ID", writeTable = TRUE)
experimentName |
an object of class tssObject with occupied
data slots @tsrData (and/or @tsrDataMerged).
The tssObject must alrady have an annotation attached to the slot
@annotation, which is provided by either
|
tsrSetType |
Specifies the type of TSR set to be processed. Options are "replicates" or "merged". |
tsrSet |
Number of the data set (of type tsrSetType) to be processed. (numeric) |
upstreamDist |
the maximum distance (in bp) upstream of the selected interval necessary to associate a TSR with a given annotation. (numeric) |
downstreamDist |
the maximum distance (in bp) downstream of the start of the selected interval to associate a TSR with a given annotation. (numeric) |
feature |
Specifies the feature to be used for annotation (typically "gene" [default] or "mRNA" for GFF3 input); set to "all" if all annotations from the input are to be used. (character) |
featureColumnID |
Name of the column identifier in the GRanges annotation object. This should be "ID" (default) for GFF3 input or "name" for bed input. (character) |
writeTable |
logical, specifying whether the output should be written to a tab-delimited file. Defaults to TRUE. |
addAnnotationToTSR adds feature annotation to the (merged) @tsrData data frame and returns the updated tssObject.
An example similar to the this one can be found in the vignette (/inst/doc/TSRchitect.Rmd)
load(system.file("extdata", "tssObjectExample.RData", package="TSRchitect")) tssObjectExample <- addAnnotationToTSR(experimentName=tssObjectExample, tsrSetType="merged", tsrSet=1, upstreamDist=1000, downstreamDist=200, feature="transcript", featureColumnID="ID", writeTable=FALSE) #if the object attached to @annotation is a gff/gff3 file