tSVE: The Shiny Variant Explorer (tSVE) web-application
In TVTB: TVTB: The VCF Tool Box

Description Usage Arguments Value Author(s) References See Also Examples

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).

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
)

`...`	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.