MTIList-class: Class "MTIList": list of miRNA target gene interaction

In jotsetung/mirtarbase: mirtarbase: a database of validated miRNA target gene interactions

Description

The class “MTIList” extends the SimpleList class from the S4Vectors package and thus allows to store a collection of MTI objects. In addition, all functions applicable to a list can be used to this type of object.

Objects from the Class

Objects should be created using the function MTIList.

Methods

as.data.frame( x, collapse.reports=NULL, stringsAsFactors=getOption( "stringsAsFactors", TRUE ), ... )

Casts the MTIList object into a data.frame. If collapse.reports is not NULL, the values from the internal Report classes will be collapsed (separated by the value of collapse.reports) resulting in a data.frame with a single row for the MTI object. Otherwise, the data.frame will have as many rows as there are Report objects in the MTI object.

entrezid( object, ... )

Returns a character vector of the NCBI Entrezgene identifier of the target gene of each MTI object in the list.

experiments( object, ... )

Returns a list with the experiments that were performed to proof the interaction for each MTI object in the list.

gene( object, ... )

Returns a character vector with the official symbol of the target gene of each MTI object in the list.

geneSpecies( object, ... )

Returns a character vector with the species of the target gene of each MTI object in the list.

id( object, ... )

Returns a character vector with the identifier of each MTI object in the list.

matmirna( object, ... )

Returns a character vector with the name of the mature miRNA of each MTI object in the list.

mirnaSpecies( object, ... )

Returns a character vector with the species of the miRNA of each MTI object in the list.

pmid( object, ... )

Returns a list of the PubMed identifier(s) of the publications providing evidence of the interaction for each MTI object in the list.

reportCount( object, ... )

Returns a numeric vector with the number of publications/reports providing evidence for each interaction in the list.

show( object )

Print the content of the MTIList class.

supportedBy( object, ... )

Returns a list of the support type of the evidence/experiments for each MTI object in the list.

Retrieve annotations (from the mirbase.db package) for the mature miRNA.

premirna( object, ... )

Returns a list with the the pre-miRNA name (i.e. the miRNA id) for the mature miRNA from the mirbase for each MTI object in the list.

mirfam( object, ... )

Returns a character vector of the miRNA family name for the mature miRNA from the mirbase for each MTI object in the list.

Note

This object directly extends the SimpleList class from the S4Vectors package, thus any method applicable to that type of class (or the generic list) can be applied to objects of this type.

Author(s)

Johannes Rainer

See Also

MTI

Examples

## get all MTIs from the database describing an interaction
## between the genes BCL2 and BCL2L11 and miRNAs from the mir-17 family.
BCL2L11 <- mtis( mirtarbase, filter=list( GenenameFilter( c( "BCL2", "BCL2L11" ) ), MirfamFilter( "mir-17" ) ) )
BCL2L11

## what's the mature miRNAs?
matmirna( BCL2L11 )
## what's are the precursors of these miRNA
premirna( BCL2L11 )

## the gene name and the Entrezgene ID?
gene( BCL2L11 )
entrezid( BCL2L11 )

## on how many reports (publications) does this base?
reportCount( BCL2L11 )

## what evidence/support types?
supportedBy( BCL2L11 )

## what experiments:
experiments( BCL2L11 )

## cast the MTIList object into a data.frame
as.data.frame( BCL2L11 )

## into a data.frame with a single row for each MTI
as.data.frame( BCL2L11, collapse.reports=";" )

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