View source: R/sequence_features.R
isInFrame | R Documentation |
Input of this function, is the output of the function [distToCds()], or any other relative ORF frame.
isInFrame(dists)
dists |
a vector of integer distances between ORF and cds. 0 distance means equal frame |
possible outputs: 0: orf is in frame with cds 1: 1 shifted from cds 2: 2 shifted from cds
a logical vector
doi: 10.1074/jbc.R116.733899
Other features:
computeFeatures()
,
computeFeaturesCage()
,
countOverlapsW()
,
disengagementScore()
,
distToCds()
,
distToTSS()
,
entropy()
,
floss()
,
fpkm()
,
fpkm_calc()
,
fractionLength()
,
initiationScore()
,
insideOutsideORF()
,
isOverlapping()
,
kozakSequenceScore()
,
orfScore()
,
rankOrder()
,
ribosomeReleaseScore()
,
ribosomeStallingScore()
,
startRegion()
,
startRegionCoverage()
,
stopRegion()
,
subsetCoverage()
,
translationalEff()
# simple example
isInFrame(c(3,6,8,11,15))
# GRangesList example
grl <- GRangesList(tx1_1 = GRanges("1", IRanges(1,10), "+"))
fiveUTRs <- GRangesList(tx1 = GRanges("1", IRanges(1,20), "+"))
dist <- distToCds(grl, fiveUTRs)
isInFrame <- isInFrame(dist)
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