clusterUnidirectionally {CAGEfightR} | R Documentation |
Finds unidirectional Tag Clusters (TCs) with a pooled TPM above a certain threshold using a slice-reduce approach. Addtionally calculates the sum and peak position of the TCs.
clusterUnidirectionally(object, ...) ## S4 method for signature 'GenomicRanges' clusterUnidirectionally(object, pooledCutoff = 0, mergeDist = 20) ## S4 method for signature 'RangedSummarizedExperiment' clusterUnidirectionally(object, ...)
object |
GRanges or RangedSummarizedExperiment: Basepair-wise pooled CTSS. |
... |
additional arguments passed to methods. |
pooledCutoff |
numeric: Minimum pooled value to be considered as TC. |
mergeDist |
integer: Merge TCs within this distance. |
GRanges with TPM sum as the score column, and TC peak as the thick column.
Other Clustering functions: clusterBidirectionally
,
trimToPeak
,
trimToPercentiles
,
tuneTagClustering
data(exampleCTSSs) # Calculate pooledTPM, using supplied number of total tags exampleCTSSs <- calcTPM(exampleCTSSs, inputAssay='counts', outputAssay='TPM', totalTags='totalTags') exampleCTSSs <- calcPooled(exampleCTSSs, inputAssay='TPM') # Cluster using defaults: slice-threshold of 0 and reduce-distance of 20 clusterUnidirectionally(exampleCTSSs) # Use custom thresholds: clusterUnidirectionally(exampleCTSSs, pooledCutoff=1, mergeDist=25)