getSeqInfoFromVariation {VarCon} | R Documentation |
This function collects information about genomic context of sequence variants.
getSeqInfoFromVariation(referenceDnaStringSet, transcriptID, variation, ntWindow=20, transcriptTable,gene2transcript=gene2transcript)
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. |
List of informations about the entered variation.
#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)