R: Unidirectional Clustering (Tag Clustering) of pooled CTSSs.

clusterUnidirectionally {CAGEfightR}

R Documentation

Unidirectional Clustering (Tag Clustering) of pooled CTSSs.

Description

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.

Usage

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, ...)

Arguments

`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.

Value

GRanges with TPM sum as the score column, and TC peak as the thick column.

Examples

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)