quantilePositions {CAGEr} | R Documentation |
Calculates the positions of “upper” and “lower” quantiles of CAGE signal along tag clusters or consensus clusters in each sample of a CAGEr object.
quantilePositions( object, clusters = c("tagClusters", "consensusClusters"), qLow = 0.1, qUp = 0.9, useMulticore = FALSE, nrCores = NULL ) ## S4 method for signature 'CAGEr' quantilePositions( object, clusters = c("tagClusters", "consensusClusters"), qLow = 0.1, qUp = 0.9, useMulticore = FALSE, nrCores = NULL )
object |
A |
clusters |
Either |
qLow, qUp |
Which “lower” or “upper” quantiles should be
calculated. Numeric vector of values in range |
useMulticore |
Logical, should multicore be used.
|
nrCores |
Number of cores to use when |
From the 5' end the position, the position of a quantile q is detemined as the first base in which of the cumulative expression is higher or equal to q% of the total CAGE signal of that cluster. Promoter interquantile width is defined as the distance (in base pairs) between a “lower” and an “upper” quantile position.
Returns the objects, in wich the positions of the quantiles are defined
reliatively to the start point of their cluster, for more efficient
Rle
compression. The quantile data for tag clusters are stored
in the TagClusters
objects directly. The quantile data for
consensus clusters are stored in integer
matrices named
“q_x”, where x represents the quantile (for instance,
q_0.1
), and these matrices are assays of the
consensusClusters
RangedSummarizedExperiment
.
Vanja Haberle
Other CAGEr object modifiers:
CTSStoGenes()
,
CustomConsensusClusters()
,
aggregateTagClusters()
,
annotateCTSS()
,
clusterCTSS()
,
cumulativeCTSSdistribution()
,
getCTSS()
,
normalizeTagCount()
,
summariseChrExpr()
Other CAGEr clusters functions:
CTSSclusteringMethod()
,
CTSScumulativesTagClusters()
,
CustomConsensusClusters()
,
aggregateTagClusters()
,
clusterCTSS()
,
consensusClustersDESeq2()
,
consensusClustersGR()
,
cumulativeCTSSdistribution()
,
plotInterquantileWidth()
,
tagClustersGR()
quantilePositions(exampleCAGEexp, "tagClusters", qLow = c(0.1, 0.2), qUp = c(0.8, 0.9)) tagClustersGR(exampleCAGEexp) quantilePositions(exampleCAGEexp, "consensusClusters", qLow = c(0.1, 0.2), qUp = c(0.8, 0.9))