computeFeatures {ORFik} | R Documentation

## Get all possible features in ORFik

### Description

If you want to get all the features easily, you can use this function. Each feature have a link to an article describing its creation and idea behind it. Look at the functions in the feature family to see all of them.

### Usage

    computeFeatures(
      grl,
      RFP,
      RNA = NULL,
      Gtf,
      faFile = NULL,
      riboStart = 26,
      riboStop = 34,
      orfFeatures = TRUE,
      includeNonVarying = TRUE,
      grl.is.sorted = FALSE
    )

### 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
`Gtf` | a TxDb object of a gtf file or path to gtf, gff .sqlite etc.
`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.

### Details

If you used CageSeq to reannotate your leaders, your txDB object must contain the reassigned leaders. Use [reassignTxDbByCage()] to get the txdb.

### 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: `computeFeaturesCage()`, `disengagementScore()`, `distToCds()`, `distToTSS()`, `entropy()`, `floss()`, `fpkm_calc()`, `fpkm()`, `fractionLength()`, `initiationScore()`, `insideOutsideORF()`, `isInFrame()`, `isOverlapping()`, `kozakSequenceScore()`, `orfScore()`, `rankOrder()`, `ribosomeReleaseScore()`, `ribosomeStallingScore()`, `startRegionCoverage()`, `startRegion()`, `subsetCoverage()`, `translationalEff()`

### Examples

    # Here we make an example from scratch
    # Usually the ORFs are found in orfik, which makes names for you etc.
    gtf <- system.file("extdata", "annotations.gtf",
    package = "ORFik") ## location of the gtf file
    suppressWarnings(txdb <-
                      GenomicFeatures::makeTxDbFromGFF(gtf, format = "gtf"))
    # use cds' as ORFs for this example
    ORFs <- GenomicFeatures::cdsBy(txdb, by = "tx", use.names = TRUE)
    ORFs <- makeORFNames(ORFs) # need ORF names
    # make Ribo-seq data,
    RFP <- unlistGrl(firstExonPerGroup(ORFs))
    suppressWarnings(computeFeatures(ORFs, RFP, Gtf = txdb))
    # For more details see vignettes.

[Package ORFik version 1.6.9 Index]