Package 'VarCon'

Title: VarCon: an R package for retrieving neighboring nucleotides of an SNV
Description: VarCon is an R package which converts the positional information from the annotation of an single nucleotide variation (SNV) (either referring to the coding sequence or the reference genomic sequence). It retrieves the genomic reference sequence around the position of the single nucleotide variation. To asses, whether the SNV could potentially influence binding of splicing regulatory proteins VarCon calcualtes the HEXplorer score as an estimation. Besides, VarCon additionally reports splice site strengths of splice sites within the retrieved genomic sequence and any changes due to the SNV.
Authors: Johannes Ptok [aut, cre]
Maintainer: Johannes Ptok <[email protected]>
License: GPL-3
Version: 1.15.0
Built: 2024-10-31 06:29:12 UTC
Source: https://github.com/bioc/VarCon

Help Index

Generates table with HZEI scores per nucleotide of a sequence.

Description

This function generates a table with HZEI scores per index nucleotide.

Usage

calculateHZEIperNT(seq)

Arguments

seq

Nucleotide sequence longer than 11nt and only containing bases "A", "G", "C", "T".

Value

Dataframe with HZEI value per index position.

Examples

calculateHZEIperNT("TTCCAAACGAACTTTTGTAGGGA")

Calculate MaxEntScan score of a splice site sequence

Description

This function calculates the MaxEntScan score of either splice donor or acceptor sequences.

Usage

calculateMaxEntScanScore(seqVector, ssType)

Arguments

seqVector

Character vector of nucleotide sequence of a splice site sequences. SA sequences should be 23nt long (20 intronic, 3 exonic) and splice donor sequences should be 9nt long (3 exonic, 6 intronic) only contain bases "A", "G", "C", "T".
ssType

Numeric indicator, if the entred sequence is a splice donor (5) or acceptor (3)

Value

Character vector of the MaxEntScan scores generated from the entered seqVector.

Examples

calculateMaxEntScanScore("TTCCAAACGAACTTTTGTAGGGA",3)
calculateMaxEntScanScore("GAGGTAAGT",5)

Small data frame specifying a transcript to certain genes for synonymous use.

Description

Small data frame specifying a transcript to certain genes for synonymous use.

Usage

gene2transcript

Format

data frame

gene_name

HGNC gene name

gene_ID

Ensembl gene ID

transcript_ID

Ensembl transcript ID

Examples

gene2transcript

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)

Generates table with MaxEntScan scores per potential SA position.

Description

This function generates a table with MaxEntScan scores per potential SA position.

Usage

getMaxEntInfo(seq)

Arguments

seq

Nucleotide sequence longer than 22nt and only containing bases "A", "G", "C", "T".

Value

Dataframe of potential acceptor index positons and corresponding MaxEntScan scores.

Examples

getMaxEntInfo("TTCCAAACGAACTTTTGTAGGGA")

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)

Donor sequences and their HBS

Description

Donor sequences and their HBS

Usage

hbg

Format

A data frame with columns:

seq

11nt long donor sequence

hbs

HBS of the donor sequence

Examples

hbg

Hexamers and Z scores

Description

Hexamers and Z scores

Usage

hex

Format

A data frame with columns:

seq

Sequence of the hexamer.

value

ZEI-score of the hexamer from HEXplorer.

first

First codon within the hexamer.

second

Second codon within the hexamer.

first_AA

First encoded amino acid within the hexamer (three lettre code).

second_AA

Second encoded amino acid within the hexamer (three lettre code).

AA

Both encoded amino acid within the hexamer

Examples

hex

Imports Fasta file from filepath.

Description

This function imports Fasta file of the reference genome into R enviroment as DNAStringset.

Usage

prepareReferenceFasta(filepath)

Arguments

filepath

R conform filepath to the fasta file of the reference genome to use.

Value

Creates new DNAStringSet from the object stated by the entered filepath.

Examples

## Loading exemplary DNAStringSet
 filepath <- system.file("extdata", "fastaEx.fa", package="Biostrings")
 referenceDnaStringSet <- prepareReferenceFasta(filepath)

Small DNAStringset as exemplary reference genome sequence

Description

Small DNAStringset as exemplary reference genome sequence

Usage

referenceDnaStringSet

Format

DNAStringset

width

Length of feature sequence

seq

Sequence of the feature

names

Name of the feature

Examples

referenceDnaStringSet

Start GUI of VarCon.

Description

Start graphical user interface for the VarCon application.

Usage

startVarConApp()

Value

Shiny app

Examples

## Not run: 
startVarConApp()

## End(Not run)

Small table as exemplary transcript table with exon coordinates

Description

Small table as exemplary transcript table with exon coordinates.

Usage

transCoord

Format

data frame

Gene.stable.ID

Ensembl gene ID

Transcript.stable.ID

Ensembl Transcript ID

Strand

Strand of the feature

Exon.region.start..bp.

Smalles coordinate of the exon end coordinates of a specific exon

Exon.region.end..bp.

Largest coordinate of the exon end coordinates of a specific exon

cDNA.coding.start

Start of the coding sequence

cDNA.coding.end

End of the coding sequence

CDS.start

Covered coding nucleotides start

CDS.end

Covered coding nucleotides end

Exon.rank.in.transcript

Rank of the exon within the respective transcript

Exon.stable.ID

Ensembl exon ID

Chromosome.scaffold.name

Name of the chromosome

Examples

transCoord