data.frame2report: Convert data.frames to Report classes and _vice versa_

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

Description

These function allow to create Report objects from data.frames (one Report object per line) or to export the contents of a Report object as a (single row) data.frame.

Usage

data.frame2report( x, colname.pmid="references_pmid", colname.support="support_type", colname.experiments="experiments", split="//", do.unique=TRUE )
report2data.frame( x, colname.pmid="references_pmid",
colname.support="support_type", colname.experiments="experiments",
split="//", stringsAsFactors=FALSE, row.names=NULL )

Arguments

x	the data.frame or Report object.
colname.pmid	the column name in the data.frame providing the pubmed identifiers of the publication.
colname.support	the column name in the data.frame that provides the support type information from the miRTarBase.
colname.experiments	the column name in the data.frame containing the types of experiments that have been performed.
split	character that allow to split experiments in the experiments column. By default all experiments in a publication that provide evidence for the MTI are separated by a “//”.
do.unique	by default, the function returns a unique list of Report objects, i.e. if the submitted data.frame contained several rows with the same entries for pmid, support and evidence, it will return only one Report object for these.
stringsAsFactors	whether character strings should be automatically converted to factors.
row.names	would allow to set the row.names of the data.frame.

Details

This are helper functions that allow to transform data.frames into objects and vice versa.

Value

A data.frame or a list of Report objects.

Author(s)

Johannes Rainer

See Also

data.frame2mti, mti2data.frame, Report

Examples

## get all miRNA target gene interactions (MTI) for BCL2L11 using a SQL
## query.
## Note, that we get the same MTI in multiple rows, if this MTI has been
## described in more than one publication:
con <- getMtiCon()
Res <- dbGetQuery( con, "select * from mirtarbase where target_gene='BCL2L11'" )

## the same MTI, but more than one publication.
Res[ Res$mirtarbase_id=="MIRT001206", c( "mirna", "target_gene", "references_pmid" ) ]

## create a list of Report objects.
Reps <- data.frame2report( Res )

## convert it again to a data.frame
DF <- do.call( "rbind", lapply( Reps, report2data.frame ) )
nrow( DF )

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