plotEnsemblePCA: plotEnsemblePCA

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

plotEnsemblePCA

Description

This method plots a PCA of the ensembl

Usage

plotEnsemblePCA(foldedCds, labels = TRUE, split = TRUE)

Arguments

foldedCds	rnaCrosslinkDataSet after running foldrnaCrosslink
labels	plot with labels or not (TRUE/FALSE)
split	split the plot using facets based on the samples (TRUE/FALSE)

Value

a PCA plot of the ensembl

Examples

## Not run: 
cds = makeExamplernaCrosslinkDataSet()
clusteredCds = clusterrnaCrosslink(cds = cds,
                               cores = 3,
                               stepCount = 2,
                               clusterCutoff = 1)


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



fasta = paste(c(rep('A',25),
                rep('T',25),
                rep('A',10),
                rep('T',23)),collapse = "")

header = '>transcript1'


fastaFile = tempfile()
writeLines(paste(header,fasta,sep = "\n"),con = fastaFile)


rnaRefs = list()
rnaRefs[[rnas(cds)]] = read.fasta(fastaFile)
rnaRefs



foldedCds = foldrnaCrosslink(trimmedClusters,
                         rnaRefs = rnaRefs,
                         start = 1,
                         end = 83,
                         shape = 0,
                         ensembl = 5,
                         constraintNumber  = 1,
                         evCutoff = 1)


plotEnsemblePCA(foldedCds)

## End(Not run)

JLP-BioInf/comradesOO documentation built on April 28, 2024, 4:22 a.m.