allFeaturesHelper {ORFik} | R Documentation |
Not used directly, calculates all features.
allFeaturesHelper(grl, RFP, RNA, tx, fiveUTRs, cds, threeUTRs, faFile, riboStart, riboStop, orfFeatures, includeNonVarying, grl.is.sorted)
grl |
a |
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. |
a data.table with features