trimClusters: trimClusters

In JLP-BioInf/comradesOO: Analysis of RNA Crosslinking Data

trimClusters

Description

Trimming of the clusters removes redundant information derived from random fragmentation of the reads during library preparation. This method takes a rnaCrosslinkDataSet object where clustering has been performed with the clusterrnaCrosslink method and trims the clusters according to the trimFactor argument.

Usage

trimClusters(clusteredCds, trimFactor = 2.5, clusterCutoff = 1)

Arguments

clusteredCds	a rnaCrosslinkDataSet object
trimFactor	a positive value that defines how much the clusters will
clusterCutoff	Minimum number of reads before discarding cluster be trimmed = mean + ( sd * trimFactor )

Details

The 3 attributes; matrixList, clusterTableList and clusterGrangesList will gain the types "superClusters" and "trimmedClusters"

Value

Returns a rnaCrosslinkDataSet object

Examples

cds = makeExamplernaCrosslinkDataSet()

clusteredCds = clusterrnaCrosslink(cds,
                cores = 1,
                stepCount = 1,
                clusterCutoff = 0)
                
trimClusters(clusteredCds = clusteredCds,
             trimFactor = 1, 
             clusterCutoff = 0)

JLP-BioInf/comradesOO documentation built on March 7, 2024, 11:10 p.m.