allFeaturesHelper {ORFik} | R Documentation

## Calculate the features in computeFeatures

### Description

Not used directly, calculates all features.

### Usage

    allFeaturesHelper(
      grl,
      RFP,
      RNA,
      tx,
      fiveUTRs,
      cds,
      threeUTRs,
      faFile,
      riboStart,
      riboStop,
      orfFeatures,
      includeNonVarying,
      grl.is.sorted
    )

### Arguments

`grl` | a `GRangesList` object with usually ORFs, but can also be either leaders, cds', 3' utrs, etc.
`RFP` | RiboSeq reads as GAlignment, GRanges or GRangesList object
`RNA` | RnaSeq reads as GAlignment, GRanges or GRangesList object
`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, if you used cage-data to extend 5' utrs, remember to input CAGE assigned version and not original!
`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
`orfFeatures` | a logical, is the grl a list of orfs?
`includeNonVarying` | a logical, if TRUE, include all features not dependent on RiboSeq data and RNASeq 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.

### Value

a data.table with features

[Package ORFik version 1.6.9 Index]