mirtarbase.db-package: The miRTarBase database for validated miRNA target gene...

In jotsetung/mirtarbase-db: miRTarBase miRNA-target interaction database

Description

This package provides the miRNA target gene interactions (MTI) from the miRTarBase database.

Author(s)

Johannes Rainer

Maintainer: Johannes Rainer <[e-mail]>

References

http://bioinfo.i-med.ac.at

Examples

## connect to the database:
con <- getMtiCon()
dbGetQuery( con, "select count( * ) from mirtarbase;" )

## get a MTI for the gene BCL2L11, using an SQL query
Res <- dbGetQuery( con, "select * from mirtarbase where target_gene='BCL2L11'" )

## Report stuff
## generate Report class instances from that data.frame:
Reports <- data.frame2report( Res )
## get a data.frame listing all reports for that MTI.
Reports.df <- do.call( "rbind", lapply( Reports, report2data.frame ) )

## creating MTI objects from the data.frame. Note that the report slot
## of the MTI objects will be empty.
MTIs <- data.frame2mti( Res, do.unique=FALSE )
length( MTIs )
MTIs <- data.frame2mti( Res )
length( MTIs )
## note, we do have empty report slots in these MTIs, thus the corresponding data.frame columns will also be empty.
do.call( "rbind", lapply( MTIs, mti2data.frame ) )

## the "right" way to get MTIs:
MTIs <- getMti( "BCL2L11" )
length( MTIs )

## get only MTIs for human BCL2L11
MTIs <- getMti( "BCL2L11", filter.gene.species="Homo sapiens" )
length( MTIs )

## get the miRNAs that have been reported:
lapply( MTIs, matureMirna )
## the publications
lapply( MTIs, pmid )

## The reports for a selected MTI:
reports( MTIs[[ "MIRT001206" ]] )

## transform to a data.frame. Note that the a MTI can be present in more
## than one row, depending on the number of publications.
do.call( "rbind", lapply( MTIs, mti2data.frame ) )

## with collapse.report="," mutliple evidences per MTI will be pasted,
## so each line represents a unique MTI
do.call( "rbind", lapply( MTIs, mti2data.frame, collapse.reports=", " ) )

## some annotation stuff...
## retrieving information from mirbase
getMirbaseForMature( "hsa-miR-223-3p" )

jotsetung/mirtarbase-db documentation built on May 19, 2019, 9:42 p.m.