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 = NULL, 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,
`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. In the future release reasignment will create txdb objects for you, but currently this is not supported, therefore be carefull.

### 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`, `subsetCoverage`, `translationalEff`

### Examples

    # Usually the ORFs are found in orfik, which makes names for you etc.
    # Here we make an example from scratch
    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 1.2.1 Index]