addAnnotationToTSR {TSRchitect} | R Documentation

## addAnnotationToTSR

### Description

`addAnnotationToTSR` associates an identified promoter with a given gene, if found upstream and on the same strand within a specified range.

### Usage

    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
    )

### Arguments

`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 `importAnnotationExternal` or `importAnnotationHub`.
`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.

### Value

addAnnotationToTSR adds feature annotation to the (merged) @tsrData data frame and returns the updated tssObject.

### Note

An example similar to the this one can be found in the vignette (/inst/doc/TSRchitect.Rmd)

### Examples

    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

[Package TSRchitect version 1.18.0 Index]