trimClusters: trimClusters

In comradesOO: Analysis of COMRADES (Cross-Linking Matched RNA and Deep Sequencing) Data

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)

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"

Value

Returns a comradesDataSet object

Examples

cds = makeExampleComradesDataSet()

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

comradesOO documentation built on Nov. 10, 2023, 5:08 p.m.