generateHEXplorerPlot {VarCon}R Documentation

Generates plot with HZEI values and splice site strengths from a list holding information about an SNV.

Description

This function generates a plot depicting the HZEI score changes and changes in the HBS or MaxEntScan score, from a sequence variation.

Usage

generateHEXplorerPlot(variationInfoList, ntWindow)

Arguments

variationInfoList

Output from the getSeqInfoFromVariation function.

ntWindow

Numeric value defining the sequence surrounding of interest.

Value

Plot stating the HZEI values per nt and splice site strength with and without the SNV.

Examples

#Defining exemplary input data
transcriptTable <- transCoord    # Using pseudo transcript table
transcriptID <- "pseudo_ENST00000650636"     # Using pseudo transcript 
variation <- "c.412C>G/p.(T89M)"
ntWindow <- 20
gene2transcript <- data.frame(gene_name = "Example_gene", 
gene_ID = "pseudo_ENSG00000147099", transcript_ID = "pseudo_ENST00000650636")

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

generateHEXplorerPlot(results)


[Package VarCon version 1.1.0 Index]