foldrnaCrosslink {rnaCrosslinkOO}

foldrnaCrosslink

Description

This methods folds an ensebl of structures for the whole RNA or chosen region of the RNA. See rnaCrosslinkDataSet for slot information.

Usage

foldrnaCrosslink(
  cdsObject,
  rnaRefs,
  start,
  end,
  evCutoff = 1,
  ensembl = 50,
  constraintNumber = 20,
  shape = 0
)

Arguments

cdsObject

rnaCrosslinkDataSet object created with rnaCrosslinkDataSet

rnaRefs

named List - a list with named elements that correspond to the .RNA of interest. The element of the list must be a fasta file that has been read with seqinr::read.fasta()

start

Start of segmnent to fold

end

End of segmnent to fold

evCutoff

Mininum number of read support for contraint to be included in folding

ensembl

Number of structures to Nake

constraintNumber

Number of constraints to add to each final fold

shape

shape reactivities (0 for no constraints)

Value

a rnaCrosslinkDataSet object

Examples

## Not run: 
cds = makeExamplernaCrosslinkDataSet()

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

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)
foldedCds

## End(Not run)