clusterBidirectionally {CAGEfightR} | R Documentation |
Finds sites with (balanced and divergent) bidirectional transcription using sliding windows of summed coverage: The Bhattacharyya coefficient (BC) is used to quantify depature from a perfectly balanced site, and a slice-reduce is used to identify sites.
clusterBidirectionally(object, ...) ## S4 method for signature 'GenomicRanges' clusterBidirectionally(object, window = 199, balanceThreshold = 0.95) ## S4 method for signature 'RangedSummarizedExperiment' clusterBidirectionally(object, ...)
object |
GenomicRanges or RangedSummarizedExperiment: Pooled CTSSs stored in the score column. |
... |
additional arguments passed to methods. |
window |
integer: Width of sliding window used for calculating window sums. |
balanceThreshold |
numeric: Minimum value of the BC to use for slice-reduce, a value of 1 corresponds to perfectly balanced sites. |
GRanges with bidirectional sites: Minimum width is 1 + 2*window, TPM sum (on both strands) in the score column, maximal bidirectional site in the thick column and maximum balance in the balance column.
Other Clustering functions: clusterUnidirectionally
,
trimToPeak
,
trimToPercentiles
,
tuneTagClustering
## Not run: 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: balance-treshold of 199 and window of 199 bp: clusterBidirectionally(exampleCTSSs) # Use custom thresholds: clusterBidirectionally(exampleCTSSs, balanceThreshold=0.99, window=101) ## End(Not run)