isInFrame: Find frame for each orf relative to cds

In ORFik: Open Reading Frames in Genomics

Description

Input of this function, is the output of the function [distToCds()], or any other relative ORF frame.

Usage

isInFrame(dists)

Arguments

dists

a vector of integer distances between ORF and cds. 0 distance means equal frame

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(), countOverlapsW(), disengagementScore(), distToCds(), distToTSS(), entropy(), floss(), fpkm_calc(), fpkm(), fractionLength(), initiationScore(), insideOutsideORF(), isOverlapping(), kozakSequenceScore(), orfScore(), rankOrder(), ribosomeReleaseScore(), ribosomeStallingScore(), startRegionCoverage(), startRegion(), stopRegion(), 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)
isInFrame <- isInFrame(dist)

ORFik documentation built on March 27, 2021, 6 p.m.