plotStructure {rnaCrosslinkOO} | R Documentation |
plotStructure
Description
This method plots a structures chosen from the plotEnsemblePCA method
Usage
plotStructure(foldedCds, rnaRefs, s = "s1", n = 1)
Arguments
foldedCds |
|
rnaRefs |
A fasta of the transcript (made with seqinr::read.fasta) |
s |
sample of structure |
n |
number of structure |
Value
a diagram of the predicted structure
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)
plotStructure(foldedCds,rnaRefs,"s1",3)
## End(Not run)
[Package rnaCrosslinkOO version 0.1.4 Index]