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):
columns shows which kinds of data can be returned from the
keytypes allows the user to discover which keytypes can be
passed in to
keys as the
keys returns keys from the
Mart of the type specified by
select is meant to be used with these other methods and has
arguments that take the kinds of values that these other methods
select will retrieve the results as a data.frame based
on parameters for selected
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the keys to select records for from the database. Keys
for some keytypes can be extracted by using the
the columns or kinds of things that can be retrieved
from the database. As with
the keytype that matches the keys used. For the
other arguments. These include:
keytypes each return a character
vector or possible values.
select returns a data.frame.
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## 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')
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