tuneTagClustering {CAGEfightR} | R Documentation |
This function counts the number of Tag Clusters (TCs) for an exponentially increasing series of expression cutoffs.
tuneTagClustering(object, ...) ## S4 method for signature 'GenomicRanges' tuneTagClustering(object, steps = 10L, mergeDist = 20L, searchMethod = "minUnique", maxExponent = 1) ## S4 method for signature 'RangedSummarizedExperiment' tuneTagClustering(object, ...) ## S4 method for signature 'GPos' tuneTagClustering(object, ...)
object |
GenomicRanges or RangedSummarizedExperiment: Pooled CTSS. |
... |
additional arguments passed to methods. |
steps |
integer: Number of thresholds to analyze (in addition to treshold=0). |
mergeDist |
integer: Merge TCs within this distance. |
searchMethod |
character: For advanced user only, see details. |
maxExponent |
numeric: The maximal threshold to analyse is obtained as min(score)*2^maxExponent (only used if searchMethod='exponential'). |
data.frame with two columns: threshold and nTCs (number of Tag Clusters)
Other Clustering functions: clusterBidirectionally
,
clusterUnidirectionally
,
trimToPeak
, trimToPercentiles
data(exampleCTSSs) # Calculate pooledTPM, using supplied number of total tags exampleCTSSs <- calcTPM(exampleCTSSs, inputAssay='counts', outputAssay='TPM', totalTags='totalTags') exampleCTSSs <- calcPooled(exampleCTSSs, inputAssay='TPM') # Set backend library(BiocParallel) register(SerialParam()) # Find optimal slice-threshold for reduce distance of 20: tuneTagClustering(object=exampleCTSSs)