tSVE: The Shiny Variant Explorer (tSVE) web-application

In kevinrue/TVTB: TVTB: The VCF Tool Box

The Shiny Variant Explorer (tSVE) web-application

Description

Currently unsupported — Package undergoing major updates.

This function starts the interactive tSVE shiny web-application that allows to interactively load and visualise genetic variants and their Ensembl Variant Effect Predictor (VEP) predictions using the package methods. All arguments after the ... set default values for the application (e.g. widgets).

Usage

tSVE(
    ...,
    refGT = "0|0",
    hetGT = c("0|1", "1|2", "0|2", "1|0", "2|1", "2|0"),
    altGT = c("1|1", "2|2"),
    vepKey = "CSQ",
    refSuffix = "REF", hetSuffix = "HET", altSuffix = "ALT",
    aafSuffix = "AAF", mafSuffix = "MAF",
    genoHeatmap.height = "500px",
    options.width = 120,
    autodetectGTimport = FALSE
)

Arguments

...	Additional arguments passed to the runApp function from the shiny package.
refGT	Default homozygote reference genotypes.
hetGT	Default heterozygote genotypes.
altGT	Default homozygote alternate genotypes.
vepKey	Default INFO key for the VEP prediction field.
refSuffix	Default INFO key suffix used to store the data for homozygote reference genotypes.
hetSuffix	Default INFO key suffix used to store the data for heterozygote genotypes.
altSuffix	Default INFO key suffix used to store the data for homozygote alternate genotypes.
aafSuffix	Default INFO key suffix used to store the data for alternate allele frequency.
mafSuffix	Default INFO key suffix used to store the data for minor allele frequency.
genoHeatmap.height	Default height (in pixels) of the heatmap that represents the genotype of each variant in each sample.
options.width	Sets options("width").
autodetectGTimport	Default checkbox value. If FALSE, genotypes (ref, het, alt) are taken as is from the Advanced settings panel. If TRUE, genotypes selected in the Advanced settings panel are updated using the autodetectGenotypes method, immediately after variants are imported.

Value

Not applicable (yet).

Author(s)

Kevin Rue-Albrecht

References

Interface to EnsDb adapted from the ensembldb package.

See Also

runEnsDbApp.

Examples

if (interactive()){
    runEnsDbApp()
}

kevinrue/TVTB documentation built on July 9, 2024, 11:42 p.m.