getSeqInfoFromVariation: Collects information about genomic context of sequence...

In caggtaagtat/VarCon: VarCon

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)

caggtaagtat/VarCon documentation built on Nov. 26, 2020, 7:03 a.m.