myvariant: Accesses MyVariant.info variant query and annotation services
Version 1.6.0

MyVariant.info is a comprehensive aggregation of variant annotation resources. myvariant is a wrapper for querying MyVariant.info services

AuthorAdam Mark
Bioconductor views Annotation GenomicVariation VariantAnnotation
Date of publicationNone
MaintainerAdam Mark, Chunlei Wu <cwu@scripps.edu>
LicenseArtistic-2.0
Version1.6.0
Package repositoryView on Bioconductor
InstallationInstall the latest version of this package by entering the following in R:
source("https://bioconductor.org/biocLite.R")
biocLite("myvariant")

Getting started

Package overview
README.md

Popular man pages

formatHgvs: Get all HGVS IDs from Vcf object.
formatSingleHgvs: Get Hgvs HGVS ID from chromosome, position, reference and...
getVariant: Return the variant object for the given HGVS id.
getVariants: Return the list of variant objects for the given list of HGVS...
metadata: metadata
myvariant-package: Access MyVariant.info variant annotation services
queryVariants: Return the batch query result.
See all...

All man pages Function index File listing

Man pages

formatHgvs: Get all HGVS IDs from Vcf object.
formatSingleHgvs: Get Hgvs HGVS ID from chromosome, position, reference and...
getVariant: Return the variant object for the given HGVS id.
getVariants: Return the list of variant objects for the given list of HGVS...
metadata: metadata
MyVariant: MyVariant
MyVariant-class: Class '"MyVariant"'
myvariant-package: Access MyVariant.info variant annotation services
queryVariant: Return the query result.
queryVariants: Return the batch query result.

Functions

MyVariant Man page
MyVariant-class Man page
collapse Source code
convertColumn4csv Source code
df2DF Source code
df2csv Source code
factor2List Source code
formatHgvs Man page Source code
formatSingleHgvs Man page Source code
getDels Source code
getIndels Source code
getIns Source code
getSnps Source code
getVariant Man page
getVariant,MyVariant-method Man page
getVariant,missing-method Man page
getVariants Man page
getVariants,MyVariant-method Man page
getVariants,missing-method Man page
json.batch.collapse Source code
json2df Source code
metadata Man page
metadata,MyVariant-method Man page
myvariant Man page
pop Source code
queryVariant Man page
queryVariant,MyVariant-method Man page
queryVariant,missing-method Man page
queryVariants Man page
queryVariants,MyVariant-method Man page
queryVariants,missing-method Man page
repeated.query Source code
return.as Source code
splitBySize Source code
splitCols Source code
transpose.nested.list Source code
trim Source code
uncollapse Source code
unnest Source code
unnest.df Source code
validMyVariantObject Source code

Files

DESCRIPTION
NAMESPACE
R
R/MyVariant.R
R/readHGVS.R
R/utils.R
README.md
build
build/vignette.rds
inst
inst/doc
inst/doc/myvariant.R
inst/doc/myvariant.Rnw
inst/doc/myvariant.pdf
inst/extdata
inst/extdata/dbsnp_mini.vcf
man
man/MyVariant-class.Rd
man/MyVariant.Rd
man/formatHgvs.Rd
man/formatSingleHgvs.Rd
man/getVariant.Rd
man/getVariants.Rd
man/metadata.Rd
man/myvariant-package.Rd
man/queryVariant.Rd
man/queryVariants.Rd
vignettes
vignettes/myvariant.Rnw
myvariant documentation built on May 20, 2017, 10:41 p.m.

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