Package 'GA4GHshiny'

Shiny application for interacting with GA4GH-based data servers

Description

GA4GHshiny package provides an easy way to interact with data servers based on Global Alliance for Genomics and Health (GA4GH) Genomics API through a Shiny application. It also integrates with Beacon Network.

Author(s)

Welliton Souza, Benilton Carvalho, Cristiane Rocha, Elizabeth Borgognoni

Maintainer: Welliton Souza <[email protected]>

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Open web application

Description

Web application for interacting with GA4GH API data servers.

Usage

app(host, orgDb = NA_character_, txDb = NA_character_,
  serverName = "GA4GHshiny")

Arguments

host	Character vector of an URL of GA4GH API data server endpoint.
orgDb	character vector of an org.Db package.
txDb	character vector of a TxDb package.
serverName	character vector of the server name. Default: GA4GHshiny.

Details

This application is dependent of which data the server provides trough GA4GH API. If some of tables or graphic charts not appear, the server connected may not provide the necessary data. For example, INFO data.

Value

Shiny application object.

Examples

if (interactive()) {
  library(org.Hs.eg.db)
  library(TxDb.Hsapiens.UCSC.hg19.knownGene)
  app("http://1kgenomes.ga4gh.org/", orgDb = "org.Hs.eg.db",
    txDb = "TxDb.Hsapiens.UCSC.hg19.knownGene")
}

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Count genotype

Description

Summarize a list of genotype data. Variant calls with no coverage (./.) do not enter in this count.

Usage

countGenotype(genotype)

Arguments

genotype

list of integer vectors of length 2.

Value

data.frame of 1 row containing the columns below.

• ref.homozygous reference homosygous (e.g. 0/0);

• alt.heterozygous alternate heterozygous (e.g. 0/1, 1/2);

• ref.homozygous reference homozygous (e.g. 1/1, 2/2);

• total the sum of the three previous columns.

Examples

countGenotype(genotype = list(c(0,0), c(0,1), c(1,2), c(1,1), c(2,2)))

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