mmquery_bioc-class: S4 constructor and methods for object returned by...

Description Usage Arguments Value Slots

Description

This package's primary user-facing object. Contains the SQL statement and the returned data query, as well as a summary table depending on specified option. Note that the returned data is now contained in a single dataframe. To filter to a specific type of association or interaction, select on the type variable.

Usage

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as.mmquery_bioc(.list)

## S4 method for signature 'mmquery_bioc'
columns(x)

## S4 method for signature 'mmquery_bioc'
keys(x, keytype, ...)

## S4 method for signature 'mmquery_bioc'
keytypes(x)

## S4 method for signature 'mmquery_bioc'
select(x, keys, columns, keytype, ...)

## S4 method for signature 'mmquery_bioc'
show(object)

Arguments

.list

a list of returned dataframes, summary

x, object

An mmquery_bioc object.

keytype

allows the user to discover which keytypes can be passes in to select or keys and the keytype argument

...

additional arguments

keys

A result of the keys() function. For the mmquery_bioc class this is a character vector of microRNA's in the returned mmquery_bioc object.

columns

lists the columns that can be returned for the mmquery_bioc object.

Value

an s4 object of class mmquery_bioc. Contains queried data, a summary dataset, and associated input parameters.

Slots

data

A dataframe containing validated and predicted microRNA-target interactions and disease/drug assocations found.

queries

A list of queries submitted to the multiMiR SQL server.

summary

A summary dataframe of the returned microRNA dataframes

tables

A character vector of the microRNA relationship types returned (validated, predicted, disease.drug, or all).

org

The selected organism (hsa/human, mmu/mouse, rno/rat).

predicted.cutoff

An integer giving a prediction score cutoff.

predicted.cutoff.type

A character indicating the type of prediction score cutoff (p = percentage, n = number, character() = none)

predicted.site

A character string indicating the type of predicted target sites to searched.


KechrisLab/multiMiR documentation built on May 29, 2020, 1:55 a.m.