allFeaturesHelper: Calculate the features in computeFeatures function
In Roleren/ORFik: Open Reading Frames in Genomics

allFeaturesHelper

R Documentation

Calculate the features in computeFeatures function

Description

Not used directly, calculates all features internally for computeFeatures.

Usage

allFeaturesHelper(
  grl,
  RFP,
  RNA,
  tx,
  fiveUTRs,
  cds,
  threeUTRs,
  faFile,
  riboStart,
  riboStop,
  sequenceFeatures,
  uorfFeatures,
  grl.is.sorted,
  weight.RFP = 1L,
  weight.RNA = 1L,
  st = NULL
)

Arguments

`grl`	a `GRangesList` object with usually ORFs, but can also be either leaders, cds', 3' utrs, etc. This is the regions you want to score.
`RFP`	RiboSeq reads as `GAlignments` , `GRanges` or `GRangesList` object
`RNA`	RnaSeq reads as `GAlignments` , `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 If you are using CAGE, 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 path to fasta indexed genome, an open `FaFile`, a BSgenome, or path to ORFik `experiment` with valid genome.
`riboStart`	usually 26, the start of the floss interval, see ?floss
`riboStop`	usually 34, the end of the floss interval
`sequenceFeatures`	a logical, default TRUE, include all sequence features, that is: Kozak, fractionLengths, distORFCDS, isInFrame, isOverlapping and rankInTx. uorfFeatures = FALSE will remove the 4 last.
`uorfFeatures`	a logical, default TRUE, include all uORF sequence features, that is: distORFCDS, isInFrame, isOverlapping and rankInTx
`grl.is.sorted`	logical (F), a speed up if you know argument grl is sorted, set this to TRUE.
`weight.RFP`	a vector (default: 1L). Can also be character name of column in RFP. As in translationalEff(weight = "score") for: GRanges("chr1", 1, "+", score = 5), would mean score column tells that this alignment region was found 5 times.
`weight.RNA`	Same as weightRFP but for RNA weights. (default: 1L)
`st`	(NULL), if defined must be: st = startRegion(grl, tx, T, -3, 9)