Package 'mygene'

Title: Access MyGene.Info_ services
Description: MyGene.Info_ provides simple-to-use REST web services to query/retrieve gene annotation data. It's designed with simplicity and performance emphasized. *mygene*, is an easy-to-use R wrapper to access MyGene.Info_ services.
Authors: Adam Mark, Ryan Thompson, Cyrus Afrasiabi, Chunlei Wu
Maintainer: Adam Mark, Cyrus Afrasiabi, Chunlei Wu <[email protected]>
License: Artistic-2.0
Version: 1.41.0
Built: 2024-06-30 06:30:42 UTC
Source: https://github.com/bioc/mygene

Help Index

Return the gene object for the given geneid.

Description

This is a wrapper for GET query of "/gene/<geneid>" service.

Usage

getGene(geneid, fields = c("symbol", "name", "taxid", "entrezgene"), 
        ..., return.as=c("records", "text"), mygene)

Arguments

geneid

Entrez/ensembl gene id

fields

Fields to return, a list of a comma-sep string. If fields=="all", all available fields are returned.

...

Includes species as well as several other fields. View available fields by calling ?metadata. Also, see http://docs.mygene.info/en/latest/doc/annotation_service.html for complete argument details and syntax.

return.as

"records"" (list), "text" (JSON).

mygene

A MyGene object that describes how to connect to data resources. See MyGene-class. If missing, default object will be used that accesses the main MyGene.info portal. Default is recommended.

Value

returns a gene object containing the queried annotations

References

Ref: http://docs.mygene.info/en/latest/doc/annotation_service.html

See Also

getGenes query queryMany

Examples

## return the gene object for the given gene id
getGene(1017)

## customize fields
getGene(1017, fields=c("name", "symbol", "refseq"), return.as="text")

## all fields
getGene(1017, fields="all")

Return the list of gene objects for the given list of geneids.

Description

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

Usage

getGenes(geneids, fields = c("symbol", "name", "taxid", "entrezgene"), ..., 
          return.as=c("DataFrame", "records", "text"), mygene)

Arguments

geneids

A vector, list, or comm-sep string entrez/ensembl gene ids

fields

A vector of fields to return. If fields=="all", all available fields are returned.

...

Includes species as well as several other fields. View available fields by calling ?metadata. Also, see http://docs.mygene.info/en/latest/doc/annotation_service.html for complete argument details and syntax.

return.as

"DataFrame" (default), "records" (list), "text" (JSON).

mygene

A MyGene object that describes how to connect to data resources. See MyGene-class. If missing, default object will be used that accesses the main MyGene.info portal. Default is recommended.

Value

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

References

Ref: http://docs.mygene.info/en/latest/doc/annotation_service.html

See Also

getGene query queryMany

Examples

## Return the list of gene object for the given list of gene ids.
getGenes(c(1017,1018))

## mix types of gene ids
getGenes(c(1017,1018,"ENSG00000148795"))

makeTxDbFromMyGene

Description

makeTxDbFromMyGene allows the user to make a TxDb object in the Genomic Features package from a mygene "exons" query using a default MyGene object.

Usage

makeTxDbFromMyGene(gene.list, scopes, species, returnall=FALSE)

Arguments

gene.list

A list, vector, or comma-separated string of query terms.

scopes

Type of types of identifiers, either a list, vector, or a comma-separated fields to specify type of input qterms, e.g. c("reporter", "ensembl.gene", "symbol") refer to "http://docs.mygene.info/en/latest/doc/data.html#available-fields" for full list of fields.

species

Names or taxonomy ids

returnall

Logical, if TRUE, return list of genes without exons annotations. False by Default.

Details

makeTxDbFromMyGene invokes either the query or queryMany method and passes the response to construct a TxDb object. See ?TxDb for utilizing transcript annotations.

Value

returns TxDb object

See Also

makeTxDb

Examples

xli <- c('DDX26B','CCDC83','MAST3', 'RPL11')
txdb <- makeTxDbFromMyGene(xli, scopes="symbol", species="human")

metadata

Description

Get metadata for MyGene.info services.

Usage

metadata(x, ...)

Arguments

x

MyGene object

...

MyGene object slot parameters

Value

returns the metadata including available fields, genome assemblies, sources, statistics, taxonomy, and timestamp

References

http://mygene.info/v2/metadata

Examples

## Get metadata 
mygene<-MyGene()
metadata(mygene)

## get available fields to return
metadata(mygene)$available_fields

Access MyGene.info annotation services

Description

MyGene.Info_ provides simple-to-use REST web services to query/retrieve gene annotation data. It's designed with simplicity and performance emphasized. *mygene* is an easy-to-use R wrapper to access MyGene.info services.

Details

Package: mygene
Type: Package
Version: 0.99.0
Date: 2014-04-18
License: BSD
Depends: httr jsonlite Hmisc

Author(s)

Adam Mark, Chunlei Wu

Maintainer: Chunlei Wu <[email protected]>

References

Wu C, MacLeod I, Su AI (2013) BioGPS and MyGene.info: organizing online, gene-centric information. Nucl. Acids Res. 41(D1): D561-D565. http://mygene.info/doc/annotation_service.html http://mygene.info/doc/query_service.html

MyGene

Description

Construct a MyGene object.

Usage

MyGene(...)

Arguments

...

See help page for MyGene-class

Value

MyGene object

Examples

MyGene()

Class "MyGene"

Description

R Client to access MyGene.Info annotation services

Objects from the Class

Objects can be created by calls of the form MyGene(base.url="http://mygene.info/v2", delay=1, step=1000, version=version, verbose=TRUE, debug=FALSE).

Slots

base.url:

"http://mygene.info/v2". 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

getGene(geneid, fields = c("symbol", "name", "taxid", "entrezgene"), ..., return.as=c("records", "text")):

Return the gene object for the given geneid

getGenes(geneids, fields = c("symbol", "name", "taxid", "entrezgene"), ..., return.as=c("DataFrame", "records", "text")):

Return the list of gene object for the given list of geneids.

query(q, fields=c("name", "symbol", "taxid", "entrezgene"), ..., return.as=c("DataFrame", "records", "text")):

Return the query result.

queryMany(qterms, scopes=NULL, fields=c("name", "symbol", "taxid", "entrezgene"), ..., return.as=c("DataFrame", "records", "text"), returnall=FALSE):

Return the batch query result.

metadata(x, ...):

Get metadata for MyGene.info services.

makeTxDbFromMyGene(gene.list, scopes, species, returnall=FALSE):

Make a TxDb object from transcript annotations

Author(s)

Adam Mark, Chunlei Wu, Ryan Thompson

References

Wu C, MacLeod I, Su AI (2013) BioGPS and MyGene.info: organizing online, gene-centric information. Nucl. Acids Res. 41(D1): D561-D565.

Examples

showClass("MyGene")

Return the query result.

Description

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

Usage

query(q, ..., return.as=c("DataFrame", "records", "text"), mygene)

Arguments

q

query term(s), see query syntax at http://mygene.info/doc/query_service.html#query-syntax

...

Commonly queried fields include species, fields, size as well as several other fields. View available fields by calling ?metadata. Also, see http://docs.mygene.info/en/latest/doc/query_service.html for complete argument details and syntax.

return.as

"DataFrame" (default), "records" (list), or "text" (JSON).

mygene

A MyGene object that describes how to connect to data resources. See MyGene-class. If missing, default object will be used that accesses the main MyGene.info portal. Default is recommended.

Value

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

References

Ref: http://docs.mygene.info/en/latest/doc/query_service.html

See Also

queryMany getGene getGenes

Examples

## return the query result
query("cdk2", size=5)

query("reporter:1000_at")

query("symbol:cdk2", return.as="text")

query(q="cyclin-dependent kinase", fields="uniprot")

Return the batch query result.

Description

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

Usage

queryMany(qterms, scopes=NULL, ..., return.as=c("DataFrame", "records", "text"), mygene)

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, e.g. c("reporter", "ensembl.gene", "symbol") refer to "http://mygene.info/doc/query_service.html#available_fields" for full list of fields.

...

Commonly queried fields include species, 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. Also, see http://docs.mygene.info/en/latest/doc/query_service.html for complete argument details and syntax.

return.as

"DataFrame" (default), "records" (list), "text" (JSON).

mygene

A MyGene object that describes how to connect to data resources. See MyGene-class. If missing, default object will be used that accesses the main MyGene.info portal. Default is recommended.

Value

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

References

Ref: http://docs.mygene.info/en/latest/doc/query_service.html

See Also

query getGene getGenes

Examples

## return the batch query result
queryMany(c('1053_at', '117_at', '121_at'), scopes="reporter", fields="ensembl.gene", 
          species="human", return.as="records")

queryMany(c('1053_at', '117_at', '121_at'), scopes="reporter", species=9606)

queryMany(c('DDX26B', 'CCDC83', 'MAST3', 'FLOT1'), scopes="symbol", fields="entrezgene", species="human")