plotInterquantileWidth {CAGEr} | R Documentation |
Plots histograms of the interquantile width of tag clusters or consensus clusters in each CAGE dataset.
plotInterquantileWidth(object, clusters = c("tagClusters", "consensusClusters"), tpmThreshold = 5, qLow = 0.1, qUp = 0.9, xlim = c(0, 150), ...) ## S4 method for signature 'CAGEr' plotInterquantileWidth(object, clusters = c("tagClusters", "consensusClusters"), tpmThreshold = 5, qLow = 0.1, qUp = 0.9, xlim = c(0, 150), ...)
object |
A |
clusters |
Which clusters to be used. ( |
tpmThreshold |
Exclude clusters with normalized signal |
qLow, qUp |
Position of which "lower" (resp. "upper") quantile should be used as 5' (resp. 3') boundary. See Details. |
xlim |
The x axis limits of the plot. |
... |
Additional arguments passed to |
Interquantile width is a width (in base-pairs) of the central part of the genomic
region (bounded by the positions of specified qLow
and qUp
quantiles) that
contains >= (qUp - qLow) * 100%
of the CAGE signal. Positions of specified quantiles
within each cluster have to be calculated beforehand by calling quantilePositions
function. Interquantile width is a more robust measure of the promoter width than the total
span of the region, because it takes into account the magnitude of the expression in the
region.
Vanja Haberle
Other CAGEr plot functions: hanabiPlot
,
plotAnnot
, plotCorrelation
,
plotExpressionProfiles
,
plotReverseCumulatives
Other CAGEr clusters functions: CTSSclusteringMethod
,
CTSScumulativesTagClusters
,
CustomConsensusClusters
,
aggregateTagClusters
,
clusterCTSS
,
consensusClustersDESeq2
,
consensusClustersGR
,
cumulativeCTSSdistribution
,
quantilePositions
,
tagClusters
plotInterquantileWidth( object = exampleCAGEset, clusters = "tagClusters" , tpmThreshold = 50, qLow = 0.1, qUp = 0.9) plotInterquantileWidth( exampleCAGEexp, clusters = "consensusClusters" , tpmThreshold = 50, qLow = 0.1, qUp = 0.9)