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 1.4.0 Index]