utr.annotation (version 1.0.4)

countDNAPatternOneVariant: Count the number of DNA pattern for one variant

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.