variantsToVRanges: Convert variants to VRanges.

Description Usage Arguments Value See Also Examples

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:

Usage

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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

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

Bioconductor/GoogleGenomics documentation built on May 6, 2019, 7:51 a.m.