consensusClustersGR {CAGEr} | R Documentation |
Extracts the information on consensus clusters from a CAGEr object.
consensusClustersGR(object, sample = NULL, returnInterquantileWidth = FALSE, qLow = NULL, qUp = NULL) ## S4 method for signature 'CAGEset' consensusClustersGR(object, sample = NULL, returnInterquantileWidth = FALSE, qLow = NULL, qUp = NULL) ## S4 method for signature 'CAGEexp' consensusClustersGR(object, sample = NULL, returnInterquantileWidth = FALSE, qLow = NULL, qUp = NULL) consensusClustersSE(object) ## S4 method for signature 'CAGEset' consensusClustersSE(object) ## S4 method for signature 'CAGEexp' consensusClustersSE(object) consensusClusters(object, sample = NULL, returnInterquantileWidth = FALSE, qLow = NULL, qUp = NULL) ## S4 method for signature 'CAGEr' consensusClusters(object, sample = NULL, returnInterquantileWidth = FALSE, qLow = NULL, qUp = NULL) consensusClusters(object) <- value ## S4 replacement method for signature 'CAGEset' consensusClusters(object) <- value ## S4 replacement method for signature 'CAGEexp' consensusClusters(object) <- value consensusClustersSE(object) <- value ## S4 replacement method for signature 'CAGEset,ANY' consensusClustersSE(object) <- value ## S4 replacement method for signature 'CAGEexp,RangedSummarizedExperiment' consensusClustersSE(object) <- value consensusClustersGR(object) <- value ## S4 replacement method for signature 'CAGEset' consensusClustersGR(object) <- value ## S4 replacement method for signature 'CAGEexp' consensusClustersGR(object) <- value consensusClustersSE(object) <- value ## S4 replacement method for signature 'CAGEset,ANY' consensusClustersSE(object) <- value ## S4 replacement method for signature 'CAGEexp,RangedSummarizedExperiment' consensusClustersSE(object) <- value
object |
A |
sample |
Optional. Label of the CAGE dataset (experiment, sample) for which to extract sample-specific information on consensus clusters. |
returnInterquantileWidth |
Should the interquantile width of consensus clusters in
specified sample be returned. Used only when |
qLow |
Position of which quantile should be used as a left (lower) boundary when
calculating interquantile width. Used only when |
qUp |
Position of which quantile should be used as a right (upper) boundary when
calculating interquantile width. Used only when |
value |
A |
Returns a data.frame
with information on consensus clusters, including genomic
coordinates. When sample
argument is NOT specified, total CAGE signal across all CAGE
datasets (samples) is returned in the tpm
column. When sample
argument is
specified, the tpm
column contains CAGE signal of consensus clusters in that specific
sample. When returnInterquantileWidth = TRUE
, additional sample-specific information
is returned, including position of the dominant TSS, and interquantile width of the consensus
clusters in the specified sample.
Vanja Haberle
Other CAGEr clusters functions: CTSSclusteringMethod
,
CTSScumulativesTagClusters
,
CustomConsensusClusters
,
aggregateTagClusters
,
clusterCTSS
,
consensusClustersDESeq2
,
cumulativeCTSSdistribution
,
plotInterquantileWidth
,
quantilePositions
,
tagClusters
consensusClustersGR( exampleCAGEexp, sample = 2 , returnInterquantileWidth = TRUE , qLow = 0.1, qUp = 0.9) head(consensusClusters(exampleCAGEset)) head(consensusClusters(exampleCAGEset, sample = "sample2")) cumulativeCTSSdistribution(exampleCAGEset, "consensusClusters") # Defaults in object do not fit quantilePositions(exampleCAGEset, "consensusClusters") head(consensusClusters(exampleCAGEset, sample = "sample2" , returnInterquantileWidth = TRUE , qLow = 0.1, qUp = 0.9)) head(consensusClusters(exampleCAGEexp)) consensusClustersGR(exampleCAGEexp, 2)