| 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.