variantsToVRanges: Convert variants to VRanges.

In GoogleGenomics: R Client for Google Genomics API

Description

Note that the Global Alliance for Genomics and Health API uses a 0-based coordinate system. For more detail, please see GA4GH discussions such as the following:

• https://github.com/ga4gh/schemas/issues/168

• https://github.com/ga4gh/schemas/issues/121

Usage

variantsToVRanges(variants, oneBasedCoord = TRUE, slStyle = "UCSC")

Arguments

variants	A list of R objects corresponding to the JSON objects returned by the Google Genomics Variants API.
oneBasedCoord	Convert genomic positions to 1-based coordinates.
slStyle	The style for seqnames (chrN or N or...). Default is UCSC.

Value

VRanges

See Also

Other variants converter functions: variantsToGRanges

Examples

# Authenticated on package load from the env variable GOOGLE_API_KEY.
variants1 <- getVariants(converter=variantsToVRanges)
summary(variants1)
variants2 <- variantsToVRanges(getVariants())
print(identical(variants1, variants2))

GoogleGenomics documentation built on May 2, 2019, 12:54 a.m.