foldComrades: foldComrades

In comradesOO: Analysis of COMRADES (Cross-Linking Matched RNA and Deep Sequencing) Data

foldComrades

Description

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

Usage

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

Arguments

cdsObject	comradesDataSet object created with comradesDataSet
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 comradesDataSet object

Examples

## Not run: 
cds = makeExampleComradesDataSet()

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

## End(Not run)

comradesOO documentation built on Nov. 10, 2023, 5:08 p.m.