computeFeaturesCage {ORFik} | R Documentation

## Get all possible features in ORFik

### Description

Normally dont use this function, but instead use: [computeFeatures()]

### Usage

    computeFeaturesCage(grl, RFP, RNA = NULL, Gtf = NULL, tx = NULL,
      fiveUTRs = NULL, cds = NULL, threeUTRs = NULL, faFile = NULL,
      riboStart = 26, riboStop = 34, extension = NULL, orfFeatures = TRUE,
      cageFiveUTRs = NULL, includeNonVarying = TRUE, grl.is.sorted = FALSE)

### Arguments

`grl` | a `GRangesList` object with usually ORFs, but can also be either leaders, cds', 3' utrs or ORFs are a special case, see argument tx_len
`RFP` | ribo seq reads as GAlignment, GRanges or GRangesList object
`RNA` | rna seq reads as GAlignment, GRanges or GRangesList object
`Gtf` | a TxDb object of a gtf file,
`tx` | a GrangesList of transcripts, normally called from: exonsBy(Gtf, by = "tx", use.names = T) only add this if you are not including Gtf file You do not need to reassign these to the cage peaks, it will do it for you.
`fiveUTRs` | fiveUTRs as GRangesList, must be original unchanged fiveUTRs
`cds` | a GRangesList of coding sequences
`threeUTRs` | a GrangesList of transcript 3' utrs, normally called from: threeUTRsByTranscript(Gtf, use.names = T)
`faFile` | a FaFile or BSgenome from the fasta file, see ?FaFile
`riboStart` | usually 26, the start of the floss interval, see ?floss
`riboStop` | usually 34, the end of the floss interval
`extension` | a numeric/integer needs to be set! set to 0 if you did not use cage, if you used cage to change tss' when finding the orfs, standard cage extension is 1000
`orfFeatures` | a logical, is the grl a list of orfs? Must be assigned.
`cageFiveUTRs` | a GRangesList, if you used cage-data to extend 5' utrs, include this, also extension must match with the extension used for these.
`includeNonVarying` | a logical T, if TRUE, include all features not dependent on Ribo-seq data and RNA-seq data, that is: Kozak, fractionLengths, distORFCDS, isInFrame, isOverlapping and rankInTx
`grl.is.sorted` | logical (F), a speed up if you know argument grl is sorted, set this to TRUE.

### Details

A specialized version if you used Cage data, and don't have a new txdb with reassigned leaders, transcripts and gene starts. If you do have a txdb with cage reassignments, use computeFeatures instead. Each feature have a link to an article describing feature, try ?floss

### Value

a data.table with scores, each column is one score type, name of columns are the names of the scores, i.g [floss()] or [fpkm()]

### See Also

Other features: `computeFeatures`, `disengagementScore`, `distToCds`, `entropy`, `floss`, `fpkm_calc`, `fpkm`, `fractionLength`, `insideOutsideORF`, `isInFrame`, `isOverlapping`, `kozakSequenceScore`, `orfScore`, `rankOrder`, `ribosomeReleaseScore`, `ribosomeStallingScore`, `subsetCoverage`, `translationalEff`

### Examples

     # a small example without cage-seq data:
     # we will find ORFs in the 5' utrs
     # and then calculate features on them
     ## Not run:
     if (requireNamespace("BSgenome.Hsapiens.UCSC.hg19")) {
      library(GenomicFeatures)
      # Get the gtf txdb file
      txdbFile <- system.file("extdata", "hg19_knownGene_sample.sqlite",
      package = "GenomicFeatures")
      txdb <- loadDb(txdbFile)

      # Extract sequences of fiveUTRs.
      fiveUTRs <- fiveUTRsByTranscript(txdb, use.names = TRUE)[1:10]
      faFile <- BSgenome.Hsapiens.UCSC.hg19::Hsapiens
      # need to suppress warning because of bug in GenomicFeatures, will
      # be fixed soon.
      tx_seqs <- suppressWarnings(extractTranscriptSeqs(faFile, fiveUTRs))

      # Find all ORFs on those transcripts and get their genomic coordinates
      fiveUTR_ORFs <- findMapORFs(fiveUTRs, tx_seqs)
      unlistedORFs <- unlistGrl(fiveUTR_ORFs)
      # group GRanges by ORFs instead of Transcripts
      fiveUTR_ORFs <- groupGRangesBy(unlistedORFs, unlistedORFs$names)

      # make some toy ribo seq and rna seq data
      starts <- unlistGrl(ORFik:::firstExonPerGroup(fiveUTR_ORFs))
      RFP <- promoters(starts, upstream = 0, downstream = 1)
      score(RFP) <- rep(29, length(RFP)) # the original read widths

      # set RNA seq to duplicate transcripts
      RNA <- unlistGrl(exonsBy(txdb, by = "tx", use.names = TRUE))

      cageNotUsed <- 0 # used to inform that no cage was used

      computeFeaturesCage(grl = fiveUTR_ORFs, orfFeatures =  TRUE, RFP = RFP,
       RNA = RNA, Gtf = txdb, faFile = faFile, extension = cageNotUsed)

    }
    # See vignettes for more examples

    ## End(Not run)

[Package ORFik version 1.0.0 Index]