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Retrieve information from the BioMart databases

Source: R/methods-Mart.R
select-methods.Rd

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.

Usage

# S4 method for class 'Mart'
keys(x, keytype, ...)

# S4 method for class 'Mart'
keytypes(x)

# S4 method for class 'Mart'
columns(x)

# S4 method for class 'Mart'
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.

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)

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.

Value

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

Details

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.

Author

Marc Carlson

Examples

if (FALSE) { # interactive()
## 1st create a Mart object and specify the dataset
mart <- useEnsembl(
  biomart = "ENSEMBL_MART_ENSEMBL",
  dataset = "hsapiens_gene_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')
}