Find frame for each orf relative to cds

Description

Input of this function, is the output of the function [distToCds()]

Usage

isInFrame(dists)

Arguments

Details

possible outputs: 0: orf is in frame with cds 1: 1 shifted from cds 2: 2 shifted from cds

Value

a logical vector

References

doi: 10.1074/jbc.R116.733899

See Also

Other features: computeFeaturesCage, computeFeatures, disengagementScore, distToCds, entropy, floss, fpkm_calc, fpkm, fractionLength, insideOutsideORF, isOverlapping, kozakSequenceScore, orfScore, rankOrder, ribosomeReleaseScore, ribosomeStallingScore, subsetCoverage, translationalEff

Examples

# 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, extension = 0)
isInFrame <- isInFrame(dist)