MTI-class: Class "MTI": miRNA target gene interaction

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

Description

The class “MTI” describes a miRNA target gene interaction as provided by the miRTarBase.

Objects from the Class

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

Slots

id

The miRTarBase identifier of the interaction.

mature_mirna

The (mirbase conform) mature miRNA identifier (e.g. “hsa-mir-24-3p”).

query

Not used yet.

report

A list of MTIReport objects providing the evidence for the miRNA target gene interaction.

species_mirna

The species of the miRNA.

species_target_gene

The species of the target gene.

target_gene

The official gene symbol of the target gene.

target_gene_entrezid

The NCBI Entrezgene identifier of the target gene.

Methods

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

Casts the MTI object into a data.frame. If collapse.reports is not NULL, the values from the internal MTIReport 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 MTIReport objects in the MTI object.

entrezid(object, ...)

Returns the NCBI Entrezgene identifier of the target gene.

experiments(object, ...)

Returns the experiments that were performed to proof the interaction.

gene(object, ...)

Returns the official symbol of the target gene.

geneSpecies(object, ...)

Returns the species of the target gene.

id(object, ...)

Returns the identifier.

matmirna(object, ...)

Returns the name of the mature miRNA.

mirnaSpecies(object, ...)

Returns the species of the miRNA.

pmid(object, ...)

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

reportCount(object, ...)

Returns the number of publications/reports providing evidence for the interaction.

reports(x, ...), reports(x) <- value

Getter and setter method of the report slot. Returns a list of MTIReport objects; value should be a list of MTIReport objects or a single object.

show(object)

Print the content of the MTI class.

supportedBy(object, ...)

Returns the support type of the evidence/experiments.

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

matmirnaId(object, ...)

Returns the identifier (accession) of the mature miRNA from the mirbase.

premirna(object, ...)

Returns the pre-miRNA name (i.e. the miRNA id) for the mature miRNA from the mirbase.

premirnaId(object, ...)

Returns the pre-miRNA accession for the mature miRNA from the mirbase.

mirfam(object, ...)

Returns the miRNA family name for the mature miRNA from the mirbase.

Note

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

Author(s)

Johannes Rainer

See Also

MTIReport

Examples

## get an MTI from the database that represents 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

## what's the mature miRNA?
matmirna(BCL2L11)
## what's the precursor of this 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)

## list the reports:
reports(BCL2L11)

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

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

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