Description Usage Arguments Value See Also Examples
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.
1 2 3 4 5 6 7 8 9 10 | clusterUnidirectionally(object, ...)
## S4 method for signature 'GRanges'
clusterUnidirectionally(object, pooledCutoff = 0, mergeDist = 20L)
## S4 method for signature 'RangedSummarizedExperiment'
clusterUnidirectionally(object, ...)
## S4 method for signature 'GPos'
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()
1 2 3 4 5 6 7 8 9 10 11 12 13 14 | 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)
|
Add the following code to your website.
For more information on customizing the embed code, read Embedding Snippets.