addAnnotationToTSR-methods: *addAnnotationToTSR*

In TSRchitect: Promoter identification from large-scale TSS profiling data

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

TSRchitect documentation built on Nov. 8, 2020, 8:11 p.m.