comradesOO (version 0.1.1)

trimClusters: trimClusters

Description

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

Usage

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

Value

Returns a comradesDataSet object

Arguments

clusteredCds

a comradesDataSet 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"

Examples

cds = makeExampleComradesDataSet()

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