biomaRt: select – R documentation

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select

Retrieve information from the BioMart databases

Description

select, columns and keys are used together to extract data from a Mart object. These functions work much the same as the classic biomaRt functions such as getBM etc. and are provide here to make this easier for people who are comfortable using these methods from other Annotation packages. Examples of other objects in other packages where you can use these methods include (but are not limited to): ChipDb, OrgDb GODb, InparanoidDb and ReactomeDb.

columns shows which kinds of data can be returned from the Mart object.

keytypes allows the user to discover which keytypes can be passed in to select or keys as the keytype argument.

keys returns keys from the Mart of the type specified by it's keytype argument.

select is meant to be used with these other methods and has arguments that take the kinds of values that these other methods return. select will retrieve the results as a data.frame based on parameters for selected keys and columns and keytype arguments.

Usage

columns(x)
  keytypes(x)
  keys(x, keytype, ...)
  select(x, keys, columns, keytype, ...)

Arguments

`x`	the `Mart` object. The dataset of the `Mart` object must already be specified for all of these methods.
`keys`	the keys to select records for from the database. Keys for some keytypes can be extracted by using the `keys` method.
`columns`	the columns or kinds of things that can be retrieved from the database. As with `keys`, all possible columns are returned by using the `columns` method.
`keytype`	the keytype that matches the keys used. For the `select` methods, this is used to indicate the kind of ID being used with the keys argument. For the `keys` method this is used to indicate which kind of keys are desired from `keys`
`...`	other arguments. These include: pattern: the pattern to match (used by keys) column: the column to search on. This is used by keys and is for when the thing you want to pattern match is different from the keytype, or when you want to simply want to get keys that have a value for the thing specified by the column argument. fuzzy: TRUE or FALSE value. Use fuzzy matching? (this is used with pattern by the keys method)

Value

keys,columns and keytypes each return a character vector or possible values. select returns a data.frame.

Author(s)

Marc Carlson

Examples

## 1st create a Mart object and specify the dataset
mart<-useMart(dataset="hsapiens_gene_ensembl",biomart='ensembl')
## you can list the keytypes
keytypes(mart)
## you can list the columns
columns(mart)
## And you can extract keys when this is supported for your keytype of interest
k = keys(mart, keytype="chromosome_name")
head(k)
## You can even do some pattern matching on the keys
k = keys(mart, keytype="chromosome_name", pattern="LRG")
head(k)
## Finally you can use select to extract records for things that you are
## interested in.
affy=c("202763_at","209310_s_at","207500_at")
select(mart, keys=affy, columns=c('affy_hg_u133_plus_2','entrezgene_id'),
  keytype='affy_hg_u133_plus_2')

biomaRt

Interface to BioMart databases (i.e. Ensembl)

v2.46.3

Artistic-2.0

Authors

Steffen Durinck [aut], Wolfgang Huber [aut], Sean Davis [ctb], Francois Pepin [ctb], Vince S Buffalo [ctb], Mike Smith [ctb, cre] (<https://orcid.org/0000-0002-7800-3848>)

Initial release