computeFeatures {ORFik} | R Documentation |
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.
computeFeatures(grl, RFP, RNA = NULL, Gtf, faFile = NULL, riboStart = 26, riboStop = 34, orfFeatures = TRUE, includeNonVarying = TRUE, grl.is.sorted = FALSE)
grl |
a |
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. |
If you used CageSeq to reannotate your leaders, your txDB object must contain the reassigned leaders. Use [reassignTxDbByCage()] to get the txdb.
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()]
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
# 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.