foldrnaCrosslink: foldrnaCrosslink

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

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)

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