Function reference • genecovr

genecovr

AlignmentPairs(): Representation of an alignment pair

AlignmentPairsList(): List of AlignmentPairs instances

as.data.frame(<AlignmentPairsList>): as.data.frame

autoplot(<AlignmentPairsList>): autoplot.AlignmentPairsList

breadthOfCoverage(): breadthOfCoverage

countSubjectsByCoverage(): countSubjectsByCoverage

deletions(): Get deletions from an alignment.

divergence(): Get divergence from an alignment

geneBodyCoverage(): Get gene body coverage

insertions(): Get insertions from an alignment

matches() mismatches() repmatches(): matches

plot(<AlignmentPairsList>): plot

psl methods: methods-psl

query() `query<-`(): Retrieve query from object

readFastaIndex(): readFastaIndex

readPsl(): readPsl

reduceHitCoverage(): reduceHitCoverage

sbjct() `sbjct<-`(): Retrieve subject from object

score(): Retrieve score from object

sequence data methods: methods-sequence-data

summarizeGeneBodyCoverage(): summarizeGeneBodyCoverage