clusterBidirectionally: Bidirectional clustering of pooled CTSSs.

In MalteThodberg/CAGEfightR: Analysis of Cap Analysis of Gene Expression (CAGE) data using Bioconductor

Description

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.

Usage

clusterBidirectionally(object, ...)

## S4 method for signature 'GRanges'
clusterBidirectionally(
  object,
  window = 201,
  balanceThreshold = 0.95,
  balanceFun = balanceBC
)

## S4 method for signature 'GPos'
clusterBidirectionally(object, ...)

## S4 method for signature 'RangedSummarizedExperiment'
clusterBidirectionally(object, ...)

Arguments

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.
balanceFun	function: Advanced users may supply their own function for calculating the balance score instead of the the default balanceBC. See details for instructions.

Value

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.

See Also

Other Clustering functions: clusterUnidirectionally(), trimToPeak(), trimToPercentiles(), tuneTagClustering()

Examples

## 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)

MalteThodberg/CAGEfightR documentation built on Sept. 11, 2021, 4:42 a.m.