isInFrame {ORFik} | 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 distances between ORF and cds |
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: computeFeaturesCage
,
computeFeatures
,
disengagementScore
,
distToCds
, distToTSS
,
entropy
, floss
,
fpkm_calc
, fpkm
,
fractionLength
,
initiationScore
,
insideOutsideORF
,
isOverlapping
,
kozakSequenceScore
, orfScore
,
rankOrder
,
ribosomeReleaseScore
,
ribosomeStallingScore
,
startRegionCoverage
,
startRegion
, 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)