allFeaturesHelper: Calculate the features in computeFeatures function

Description Usage Arguments Value

View source: R/compute_Features.R

Description

Not used directly, calculates all features internally for computeFeatures.

Usage

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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)

Value

a data.table with features


ORFik documentation built on March 27, 2021, 6 p.m.