MirnaDb-class {miRNAtap} | R Documentation |
object of MirnaDb
class holds the sqlite database
connection, and extends AnnotationDb
class from AnnotationDbi
package. columns
, keys
, keytypes
and select
methods allow access to database tables and retrieval of miRNA target
information.
select
is the most important method, allows querying the
database for predictions from a specific source and species for a
given miRNA
columns(x) keytypes(x) keys(x, keytype, ...) select(x, keys, columns, keytype, ...) ## S4 method for signature 'MirnaDb' columns(x) ## S4 method for signature 'MirnaDb' keytypes(x) ## S4 method for signature 'MirnaDb' keys(x, keytype, ...) ## S4 method for signature 'MirnaDb' select(x, keys, columns, keytype, ...)
x |
the |
keytype |
the keytype that matches the keys used; the table in which the search should be performed. |
... |
any optional arguments |
keys |
the key to select records for from the database - miRNA name;
all possible keys (miRNAs) are returned by using the |
columns |
in this case same as |
string vectors, for select
a data.frame with target
genes and scores
Maciej Pajak m.pajak@sms.ed.ac.uk
#first load the annotations require(miRNAtap.db) #see all available tables keytypes(miRNAtap.db)