Report-class: Class "MTIReport", report and evidence for a miRNA target...

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

Description

The class “MTIReport” provides the evidence (i.e. the publication with all of the performed experiments of the interaction) for a miRNA target gene interaction as defined by the miRTarBase.

Objects from the Class

Objects can be created by calls of the form new("MTIReport", ...) or using the MTIReport function (the preferred way).

Slots

pmid

The PubMed identifier of the publication in which the miRNA target gene interaction has been described.

experiments

A character vector of experiments that have been performed in the publication to verify the MTI.

support_type

The evidence grade of the interaction.

Methods

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

Cast the MTIReport object into a (single row) data.frame.

show(object)

Print the content of the MTIReport class.

pmid(object, ...)

Returns the PubMed identifier(s) of the publications providing evidence of the interaction.

experiments(object, ...)

Returns the experiments that were performed to proof the interaction.

supportedBy(object, ...)

Returns the support type of the evidence/experiments.

Note

Instead of directly accessing the slots of the class, the getter methods listed above should be used.

Author(s)

Johannes Rainer

See Also

MTI

Examples

## Get an MTI from the database we're looking here for an interaction
## between the gene BCL2L11 and miRNAs from the mir-17 family.
BCL2L11 <- mtis(mirtarbase, filter=list(GenenameFilter("BCL2L11"), MirfamFilter("mir-17")))
BCL2L11 <- BCL2L11[[1]]
BCL2L11

## List the reports:
reports(BCL2L11)

## Get the first one
Rep <- reports(BCL2L11)[[1]]

Rep

## Get the support type:
supportedBy(Rep)

## Experiments
experiments(Rep)

## pubmed id
pmid(Rep)

## Cast the MTIReport object into a (single row) data.frame
as.data.frame(Rep)

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