getSeqInfoFromVariation {VarCon} | R Documentation

## Collects information about genomic context of sequence variants.

### Description

This function collects information about genomic context of sequence variants.

### Usage

    getSeqInfoFromVariation(referenceDnaStringSet, transcriptID,
    variation, ntWindow=20, transcriptTable,gene2transcript=gene2transcript)

### Arguments

`referenceDnaStringSet` | DNAStringset from the reference genome fasta file.
`transcriptID` | Ensembl ID of the transcript of interest.
`variation` | A sequence variation either refering to coding sequence or the genomic sequence (c.12A>T, or g.182284A>T).
`ntWindow` | Numeric value defining the sequence surrounding of interest.
`transcriptTable` | Table of transcrits and their exon coordinates and CDS coordinates.
`gene2transcript` | Gene to transcript conversion table with the gene name in the first column and the gene ID in the second and the transcript ID in the third column.

### Value

List of informations about the entered variation.

### Examples

    #Defining exemplary input data
    transcriptTable <- transCoord
    transcriptID <- "pseudo_ENST00000650636"
    variation <- "c.412C>G/p.(T89M)"
    gene2transcript <- data.frame(gene_name = "Example_gene",
    gene_ID = "pseudo_ENSG00000147099", transcriptID = "pseudo_ENST00000650636")

    results <- getSeqInfoFromVariation(referenceDnaStringSet, transcriptID,
    variation, ntWindow=20, transcriptTable, gene2transcript=gene2transcript)

    #Using a predefined gene to transcript conversion
    transcriptID <- "Example_gene"
    results <- getSeqInfoFromVariation(referenceDnaStringSet, transcriptID,
    variation, ntWindow=20, transcriptTable, gene2transcript=gene2transcript)

[Package VarCon version 1.2.0 Index]