compareKnown: compareKnown

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

compareKnown

Description

This method compares the current object to a know structure.run trimClusters() on the rnaCrosslinkDataSet first

Usage

compareKnown(trimmedClusters, knownMat, type)

Arguments

trimmedClusters	a rnaCrosslinkDataSet object, run trimClusters() on the rnaCrosslinkDataSet first
knownMat	Matrix - A marix(ncol = lengthRNA,nrow = lengthRNA) where a value in matrix[x,y] would indicate a known interation between nucleotide x and nucleotide y
type	string - the Analysis stage of clusters you would like to compare you can find available types by just running the objects name

Value

Returns a rnaCrosslinkClusteredDataSet object

The 3 attributes matrixList, clusterTableList and clusterGrangesList will gain the types "known" and "novel" and "knownAndNovel"

Examples

cds = makeExamplernaCrosslinkDataSet()

clusteredCds = clusterrnaCrosslink(cds,
                cores = 1,
                stepCount = 1,
                clusterCutoff = 0)
knownMat = matrix(0, ncol = rnaSize(cds), nrow = rnaSize(cds))
knownMat[7,27] = 1
# use compare known to gett he known and not know clusters
knowClusteredCds = compareKnown(clusteredCds,
                                knownMat,
                                "original")
clusterNumbers(knowClusteredCds)                 
                

JLP-BioInf/comradesOO documentation built on Aug. 11, 2024, 4:23 a.m.