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 1.4.0 Index]