Package 'myvariant'

Get all HGVS IDs from Vcf object.

Description

Read in a Vcf object created by readVcf to extract all HGVS IDs for querying MyVariant.info.

Usage

formatHgvs(vcf, variant_type = c("snp", "insertion", "deletion"))

Arguments

vcf	Vcf object created by readVcf.
variant_type	Type of variant HGVS IDs to retrieve from Vcf object. Default c("snp", "insertion", "deletion")

Value

vector

References

https://myvariant.info http://www.hgvs.org/mutnomen/recs-DNA.html

See Also

formatSingleHgvs

Examples

## return HGVS IDs for all snps in a Vcf
file.path <- system.file("extdata", "dbsnp_mini.vcf", package="myvariant")
vcf <- readVcf(file.path, genome="hg19")
hgvs <- formatHgvs(vcf, variant_type="snp")

---

Get Hgvs HGVS ID from chromosome, position, reference and alternate alleles.

Description

Create a single HGVS ID for a variant from chromosome, position, reference and alternate alleles.

Usage

formatSingleHgvs(chrom, pos, ref, alt, mutant_type=FALSE)

Arguments

chrom	Chromosome.
pos	Position of the variant on the reference genome (hg19).
ref	Reference allele.
alt	Alternate allele.
mutant_type	Logical indicating whether to return the type of mutation along with the HGVS ID.

Value

returns a string

References

https://myvariant.info http://www.hgvs.org/mutnomen/recs-DNA.html

See Also

formatHgvs

Examples

## return HGVS ID for a variant
formatSingleHgvs(1, 35367, "G", "A")

---

Return the variant object for the given HGVS id.

Description

This is a wrapper for GET query of "/variant/<hgvsid>" service.

Usage

getVariant(hgvsid, fields=NULL, 
        ..., return.as=c("records", "text"), myvariant)

Arguments

hgvsid	HGVS id
fields	Fields to return, a list of a comma-sep string. If fields=="all", all available fields are returned.
...
return.as	"records"" (list), "text" (JSON).
myvariant	A MyVariant object that describes how to connect to data resources. See MyVariant-class. If missing, default object will be used that accesses the main MyVariant.info portal. Default is recommended.

Value

returns a variant object containing the queried annotations

References

http://docs.myvariant.info/en/latest/doc/variant_annotation_service.html#get-request http://docs.myvariant.info/en/latest/doc/variant_annotation_service.html#query-parameters

See Also

getVariants queryVariant queryVariants

Examples

## return the variant object for the given HGVS id
getVariant("chr7:g.55241707G>T")

## customize fields
getVariant("chr7:g.55241707G>T", 
          fields=c("dbnsfp.cadd.phred", "dbnsfp.polyphen2"), 
          return.as="text")

---

Return the list of variant objects for the given list of HGVS ids.

Description

This is a wrapper for POST query of "/variant" service.

Usage

getVariants(hgvsids, fields=NULL, verbose=NULL, ..., 
          return.as=c("DataFrame", "records", "text"), myvariant)

Arguments

hgvsids	A vector, list, or comm-sep string HGVS ids
fields	A vector of fields to return. If fields=="all", all available fields are returned.
verbose	A logical turning on or off process status messages. Default = TRUE.
...
return.as	"DataFrame" (default), "records" (list), "text" (JSON).
myvariant	A MyVariant object that describes how to connect to data resources. See MyVariant-class. If missing, default object will be used that accesses the main MyVariant.info portal. Default is recommended.

Value

returns a variant object (DataFrame, list, or JSON text) containing the queried annotations

References

http://docs.myvariant.info/en/latest/doc/variant_annotation_service.html#batch-queries-via-post http://docs.myvariant.info/en/latest/doc/variant_annotation_service.html#id2

See Also

getVariants queryVariant queryVariants

Examples

## given a list of HGVS ids
vars <- c('chr1:g.866422C>T',
'chr1:g.876664G>A',
'chr1:g.69635G>C',
'chr1:g.69869T>A',
'chr1:g.881918G>A',
'chr1:g.865625G>A',
'chr1:g.879368C>A',
'chr1:g.889226C>T',
'chr1:g.879492C>G',
'chr1:g.879423T>G',
'chr1:g.881602C>T',
'chr1:g.879115C>G',
'chr1:g.69892T>C',
'chr1:g.879381C>T',
'chr1:g.878330C>G')

## Return the list of variant object for the given list of HGVS ids.
df <- getVariants(vars, fields="dbsnp, wellderly")

---

metadata

Description

Get metadata for MyVariant.info services.

Usage

metadata(x, ...)

Arguments

x	MyVariant object
...	MyVariant object slot parameters

Value

returns the metadata including available databases and number of documents.

References

http://myvariant.info/v1/metadata

Examples

## Get metadata 
myvariant<-MyVariant()
metadata(myvariant)

---

Access MyVariant.info variant annotation services

Description

MyVariant.Info provides REST web services to query/retrieve variant annotations. myvariant is an easy-to-use R wrapper to access MyVariant.info services.

Details

Package:	myvariant
Type:	Package
Version:	0.99.0
Date:	2014-12-18
License:	Artistic-2.0
Depends:	httr jsonlite Hmisc

Author(s)

Adam Mark

Maintainer: Adam Mark <[email protected]>

References

https://github.com/Network-of-BioThings/myvariant.info/wiki

---

MyVariant

Description

Construct a MyVariant object.

Usage

MyVariant(...)

Arguments

...	See help page for MyVariant-class

Value

MyVariant object

Examples

MyVariant()

---

Class "MyVariant"

Description

R Client to access MyVariant.Info annotation services

Objects from the Class

Objects can be created by calls of the form MyVariant(base.url="http://myvariant.info/v1", delay=1, step=1000, version=version, verbose=TRUE, debug=FALSE).

Slots

base.url:

"http://myvariant.info/v1". Object of class "character"

delay:

Sleep time between batch retrieval. Object of class "numeric"

step:

Batch limit. Object of class "numeric"

version:

httr package version. Object of class "character"

verbose:

Object of class "logical"

debug:

Object of class "logical"

Methods

getVariant(hgvsid, fields=NULL, ..., return.as=c("records", "text")):

Return the variant object for the given hgvsid

getVariants(hgvsids, fields=NULL, ..., return.as=c("DataFrame", "records", "text")):

Return the list of variant object for the given list of hgvsids.

queryVariant(q, fields=NULL, ..., return.as=c("DataFrame", "records", "text")):

Return the query result.

queryVariants(qterms, scopes=NULL, fields=NULL, ..., return.as=c("DataFrame", "records", "text"), returnall=FALSE):

Return the batch query result.

Author(s)

Adam Mark

References

https://github.com/Network-of-BioThings/myvariant.info/wiki

Examples

showClass("MyVariant")

---

Return the query result.

Description

This is a wrapper for GET query of "/query?q=<query>" service.

Usage

queryVariant(q, ..., return.as=c("DataFrame", "records", "text"), 
                     myvariant)

Arguments

q	query term(s).
...	Commonly queried fields include fields, size as well as several other fields. View available fields by calling ?metadata.
return.as	"DataFrame" (default), "records" (list), or "text" (JSON).
myvariant	A MyVariant object that describes how to connect to data resources. See MyVariant-class. If missing, default object will be used that accesses the main MyVariant.info portal. Default is recommended.

Value

returns a variant object (DataFrame, list, or JSON text) containing the queried annotations

References

http://docs.myvariant.info/en/latest/doc/variant_query_service.html#get-request http://docs.myvariant.info/en/latest/doc/variant_query_service.html#query-syntax

See Also

queryVariants getVariant getVariants

Examples

## return the query result
queryVariant("dbnsfp.variantname:BRCA2")

queryVariant("chr1:1-1000000")

---

Return the batch query result.

Description

This is a wrapper for POST query of "/query" service.

Usage

queryVariants(qterms, scopes=NULL, ..., 
                      return.as=c("DataFrame", "records", "text"), 
                      myvariant)

Arguments

qterms	A vector or list, or string of comma-separated query terms
scopes	Type of types of identifiers, either a list or a comma-separated fields to specify type of input qterms.
...	Commonly queried fields include fields, size as well as several other fields. returnall returns a list of all related data including duplicated and missing qterms. False by default. View available fields by calling ?metadata.
return.as	"DataFrame" (default), "records" (list), "text" (JSON).
myvariant	A MyVariant object that describes how to connect to data resources. See MyVariant-class. If missing, default object will be used that accesses the main MyVariant.info portal. Default is recommended.

Value

returns a variant object (DataFrame, list, or JSON text) containing the queried annotations

References

http://docs.myvariant.info/en/latest/doc/variant_query_service.html#batch-queries-via-post http://docs.myvariant.info/en/latest/doc/variant_query_service.html#id3

See Also

queryVariant getVariant getVariants

Examples

## return the batch query result

---