CTSScoordinates {CAGEr} | R Documentation |
CAGEr
objectExtracts the genomic coordinates of all detected TSSs from CAGEset and CAGEexp objects.
CTSScoordinates(object) ## S4 method for signature 'CAGEset' CTSScoordinates(object) ## S4 method for signature 'CAGEexp' CTSScoordinates(object) CTSScoordinatesGR(object) ## S4 method for signature 'CAGEset' CTSScoordinatesGR(object) ## S4 method for signature 'CAGEexp' CTSScoordinatesGR(object) CTSScoordinatesGR(object) <- value ## S4 replacement method for signature 'CAGEset' CTSScoordinatesGR(object) <- value ## S4 replacement method for signature 'CAGEexp' CTSScoordinatesGR(object) <- value CTSStagCountSE(object) <- value ## S4 replacement method for signature 'CAGEset' CTSStagCountSE(object) <- value ## S4 replacement method for signature 'CAGEexp' CTSStagCountSE(object) <- value
object |
A |
value |
Coordinates to update, in a format according to the function name. |
CTSScoordinates()
returns a data.frame
with genomic coordinates
of all TSSs. The pos
column contains 1-based coordinate of the TSS.
CTSScoordinatesGR
returns the coordinates as a CTSS()
object
wrapping genomic ranges. A filteredCTSSidx
column metadata will be present
if clusterCTSS()
was ran earlier.
Vanja Haberle
Charles Plessy
Other CAGEr accessor methods: CTSSclusteringMethod
,
CTSScumulativesTagClusters
,
CTSSnormalizedTpm
,
CTSStagCountTable
,
CTSStagCount
, GeneExpDESeq2
,
GeneExpSE
,
consensusClustersGR
,
genomeName
, inputFilesType
,
inputFiles
, librarySizes
,
sampleLabels
,
seqNameTotalsSE
, tagClusters
CTSS <- CTSScoordinates(exampleCAGEset) head(CTSS) CTSScoordinatesGR(exampleCAGEset)