CustomConsensusClusters {CAGEr} | R Documentation |
Intersects custom consensus clusters with the CTSS data in a
CAGEexp
object, and stores the result as a expression matrices
(raw and normalised tag counts).
CustomConsensusClusters(object, clusters, threshold = 0, nrPassThreshold = 1, thresholdIsTpm = TRUE) ## S4 method for signature 'CAGEexp,GRanges' CustomConsensusClusters(object, clusters, threshold = 0, nrPassThreshold = 1, thresholdIsTpm = TRUE)
object |
A |
clusters |
Consensus clusters in |
threshold, nrPassThreshold |
Only CTSSs with signal |
thresholdIsTpm |
Logical, is threshold raw tag count value (FALSE) or normalized signal (TRUE). |
By consensus it is meant that the clusters do not overlap.
stores the result as a new RangedSummarizedExperiment
in the
experiment
slot of the object. The assays of the new experiment are called
counts
and normalized
. An outOfClusters
column is added
to the sample metadata to reflect the number of molecules that do not have
their TSS in a consensus cluster.
Charles Plessy
Other CAGEr object modifiers: CTSStoGenes
,
aggregateTagClusters
,
annotateCTSS
, clusterCTSS
,
cumulativeCTSSdistribution
,
getCTSS
, normalizeTagCount
,
quantilePositions
,
summariseChrExpr
Other CAGEr clusters functions: CTSSclusteringMethod
,
CTSScumulativesTagClusters
,
aggregateTagClusters
,
clusterCTSS
,
consensusClustersDESeq2
,
consensusClustersGR
,
cumulativeCTSSdistribution
,
plotInterquantileWidth
,
quantilePositions
,
tagClusters
cc <- consensusClustersGR(exampleCAGEexp) CustomConsensusClusters(exampleCAGEexp, cc)