tagClusters {CAGEr} | R Documentation |
Extracts tag clusters (TCs) produced by clusterCTSS
function for
a specified CAGE experiment from a CAGEr object.
tagClusters(object, samples = NULL, returnInterquantileWidth = FALSE, qLow = NULL, qUp = NULL) ## S4 method for signature 'CAGEr' tagClusters(object, samples = NULL, returnInterquantileWidth = FALSE, qLow = NULL, qUp = NULL) tagClustersGR(object, sample = NULL, returnInterquantileWidth = FALSE, qLow = NULL, qUp = NULL) ## S4 method for signature 'CAGEset' tagClustersGR(object, sample = NULL, returnInterquantileWidth = FALSE, qLow = NULL, qUp = NULL) ## S4 method for signature 'CAGEexp' tagClustersGR(object, sample = NULL, returnInterquantileWidth = FALSE, qLow = NULL, qUp = NULL) tagClustersGR(object, samples = NULL) <- value ## S4 replacement method for signature 'CAGEset,ANY,ANY' tagClustersGR(object, samples = NULL) <- value ## S4 replacement method for signature 'CAGEexp,ANY,TagClusters' tagClustersGR(object, samples = NULL) <- value ## S4 replacement method for signature 'CAGEexp,missing,GRangesList' tagClustersGR(object, samples = NULL) <- value
object |
A |
samples |
Label of the CAGE dataset (experiment, sample) for which to extract tag clusters.
If |
returnInterquantileWidth |
Should the interquantile width for each tag cluster be returned. |
qLow, qUp |
Position of which quantile should be used as a left (lower) or right (upper)
boundary (for |
sample |
Label of one CAGE dataset (experiment, sample) for which to extract tag
clusters. (For |
value |
A |
Returns a data.frame
with genomic coordinates, position of dominant TSS, total
CAGE signal and additional information for all TCs from specified CAGE dataset (sample). If
returnInterquantileWidth = TRUE
, interquantile width for each TC is also calculated
using specified quantile positions and returned in the data frame.
Vanja Haberle
Other CAGEr accessor methods: CTSSclusteringMethod
,
CTSScoordinates
,
CTSScumulativesTagClusters
,
CTSSnormalizedTpm
,
CTSStagCountTable
,
CTSStagCount
, GeneExpDESeq2
,
GeneExpSE
, genomeName
,
inputFilesType
, inputFiles
,
librarySizes
, sampleLabels
,
seqNameTotalsSE
Other CAGEr clusters functions: CTSSclusteringMethod
,
CTSScumulativesTagClusters
,
CustomConsensusClusters
,
aggregateTagClusters
,
clusterCTSS
,
consensusClustersDESeq2
,
consensusClustersGR
,
cumulativeCTSSdistribution
,
plotInterquantileWidth
,
quantilePositions
head(tagClusters( exampleCAGEset, "sample2" , returnInterquantileWidth = TRUE, qLow = 0.1, qUp = 0.9)) tagClustersGR(exampleCAGEexp, "Zf.high", TRUE, 0.1, 0.9)