countDNAPatternOneVariant: Count the number of DNA pattern for one variant

In utr.annotation: Annotate Variants in the Untranslated Regions

Description

countDNAPattern count the number of DNA pattern for one variant

Usage

countDNAPatternOneVariant(variant, seqTable, dnaPattern, transcriptIdCol)

Arguments

variant	variant info
seqTable	sequences table containing two columns: ensembl_transcript_id and seq. seq is the sequence of the variantType region: e.g. 5' UTR sequence or 3' UTR sequence. The seqTable is output from function getSeqTable.
dnaPattern	the string pattern that you want to count, for example "ATG"
transcriptIdCol	the ensemble transcript id column

Value

number of DNA pattern of all transcripts for that variant.

utr.annotation documentation built on Aug. 23, 2021, 9:06 a.m.