## ----setup, echo=FALSE, results="hide"---------------------------------------- knitr::opts_chunk$set(tidy = FALSE, cache = FALSE, dev = "png") ## ---- eval=TRUE--------------------------------------------------------------- library(VarCon) ## Defining exemplary input data transcriptTable <- transCoord transcriptID <- "pseudo_ENST00000650636" variation <- "c.412T>G/p.(T89M)" ## ---- eval=TRUE--------------------------------------------------------------- library(VarCon) results <- getSeqInfoFromVariation(referenceDnaStringSet, transcriptID, variation, ntWindow=20, transcriptTable) results ## ---- eval=TRUE--------------------------------------------------------------- ## Define gene 2 transcript table geneName <- "Example_gene" gene2transcript <- data.frame(gene_name = "Example_gene", gene_ID = "pseudo_ENSG00000147099", transcriptID = "pseudo_ENST00000650636") ## ---- eval=TRUE--------------------------------------------------------------- ## Use function with gene name results <- getSeqInfoFromVariation(referenceDnaStringSet, geneName, variation, ntWindow=20, transcriptTable, gene2transcript=gene2transcript) results ## ----sessionInfo-------------------------------------------------------------- sessionInfo()