Package 'multiMiR'

Functions defining the category each table belongs to.

Description

One of three types: predicted, validated, or diseasedrug. Additionally two functions define characteristics of tables: those without a target column tables_wo_target and those with conserved target sites conserved_tables.

Usage

all_tables()

validated_tables()

predicted_tables()

diseasedrug_tables()

tables_wo_target()

conserved_tables()

reverse_table_lookup(.table)

table_types()

Arguments

.table

a table name

Value

Returns dataset that names that belong to the category of the function name (e.g. validated_tables() returns tables with validated miRNA-target interactions). reverse_table_lookup() does the opposite; it returns the category a given .table belongs to.

Examples

all_tables()
validated_tables()
predicted_tables()
diseasedrug_tables()
predicted_tables() %in% all_tables() # TRUE
table_types()

---

Get microRNA-target Interactions from the multiMiR Package

Description

The main function to retrieve predicted and validated miRNA-target interactions and their disease and drug associations from the multiMiR package.

Usage

get_multimir(url = NULL, org = "hsa", mirna = NULL, target = NULL,
  disease.drug = NULL, table = "validated", predicted.cutoff = NULL,
  predicted.cutoff.type = "p", predicted.site = "conserved",
  summary = FALSE, add.link = FALSE, use.tibble = FALSE, limit = NULL,
  legacy.out = FALSE)

get.multimir(url = NULL, org = "hsa", mirna = NULL, target = NULL,
  disease.drug = NULL, table = "validated", predicted.cutoff = NULL,
  predicted.cutoff.type = "p", predicted.site = "conserved",
  summary = FALSE, add.link = FALSE, use.tibble = FALSE, limit = NULL)

Arguments

url	Deprecated. The URL for queries is now defined by the package options multimir.url and multimir.queries.
org	a character string for the organism. Three organisms are supported so far: human ("hsa" (default), "human", or "Homo Sapiens"), mouse ("mmu", "mouse", or "Mus musculus"), and rat ("rno", "rat", or "Rattus norvegicus"). The organism is case insensitive.
mirna	'NULL' (default) or a character string or character vector for the mature miRNA(s). It can be the mature miRNA accession number (i.e. "MIMAT0000072"), mature miRNA ID (i.e. "hsa-miR-199a-3p"), or a combination of both (i.e. c("MIMAT0000065", "hsa-miR-30a-5p")). The character is case insensitive. *See note about the length of list supported.
target	'NULL' (default) or a character string or character vector for the target gene(s). It can be the gene symbol (i.e. c("TP53", "KRAS")), Entrez gene ID (i.e. c(578, 3845)), Ensembl gene ID (i.e. "ENSG00000171791"), or a combination of any of these identifiers (i.e. c("TP53", 3845, "ENSG00000171791")). The character is case insensitive. *See note about the length of list supported.
disease.drug	'NULL' (default) or a character string or character vector for the disease(s) and/or drug(s) (i.e. c("bladder cancer", "cisplatin")). The character is case insensitive.
table	a character string indicating which table(s) in multiMiR to search. Each table contains data from an external database. Options include "validated" (default, to search all validated tables "mirecords", "mirtarbase", and "tarbase"), "predicted" (to search all predicted tables "diana_microt", "elmmo", "microcosm", "miranda", "mirdb", "pictar", "pita", and "targetscan"), "disease.drug" (to search all disease/drug tables "mir2disease", "pharmaco_mir", and "phenomir"), "all" (to search all of the tables above), or an individual table from above.
predicted.cutoff	'NULL' (default) or an integer giving a prediction score cutoff. By default ('NULL'), the cutoff is '20' (search the top 20% if predicted.cutoff.type="p") or '300000' (search the top 300000 (or all records if total < 300000) if predicted.cutoff.type="n").
predicted.cutoff.type	a character indicating the type of prediction score cutoff. This must be either "p" (default, percentage cutoff) or "n" (number cutoff).
predicted.site	a character string indicating the type of predicted target sites to search. This can be one of the strings "conserved", "nonconserved", or "all", and can be abbreviated. This only applies to three of the predicted tables ("miranda", "pita", and "targetscan") that have conservation information of the target sites.
summary	logical. Whether to summarize the result (default = FALSE).
add.link	logical. Whether to add link to external database for each result entry.
use.tibble	logical. Whether to use the data_frame class from the tibble package for returned dataframes. The key benefit for large datasets is more restrictive printing to the console (first 10 rows and only the number of columns that will fit getOption('width')). See ?tible::data_frame for more information.
limit	a positive integer. Limits the number of records returned from each table. Useful in testing potentially large queries.
legacy.out	logical. Whether to return the Bioconductor compatible S4 object or the legacy S3 object (default=FALSE).

Details

get.multimir() has been deprecated and replaced with the get_multimir() version.

get_multimir is the main and recommended function to retrieve information from the multiMiR package. Input to the function must contain at least one of the followings: miRNA(s), target gene(s), and disease and drug term(s).

The setting of predicted.site is applicable to three ("miranda", "pita", and "targetscan") of the eight predicted tables. If predicted.site is "conserved", the function will search conserved target sites annotated by TargetScan, target sites with conservation scores greater than or equal to 0.57 (in human and rat; or 0.566 in mouse) in miRanda, and/or sites with conservation scores greater than or equal to 0.9 in PITA.

Although the summary (if summary=TRUE) can be used to find results that are recorded by combinations of different databases, please note that for predicted interactions a combination approach may not be as effective as a single algorithm because of age or quality of the tool.

Note: The length of the list supported has been increased from version1.0.1. The size is now limited to 20MB which should accommodate most requests. There is a possibility for technical reasons that the query could fail even if the list is under this limit. If this occurs it is recommended that you break up the list into smaller batches and submit them sequentially.

Value

get_multimir returns an S4 object (see ?mmquery_bioc-class containing the queried data and associated metadata. With legacy.out=FALSE (default), the data is a single dataset with association/interaction type defined by the type variable. With legacy.out=TRUE the original S3 object with 3 separate data frames ('predicted', 'validated', and 'disease_drug') is returned.

Examples

## search 'hsa-miR-18a-3p' in validated interactions in human
  example1 <- get_multimir(mirna='hsa-miR-18a-3p', summary=TRUE)
  columns(example1)
  ## target genes that are validated by Luciferase assay
  lucif <- select(example1, keytype = "type", keys = "validated", 
                  columns = columns(example1))
  lucif[grep("Luciferase", lucif$experiment), ]
  example1@summary[example1@summary[,"target_symbol"] == "KRAS",]

  ## search 'cisplatin' in disease and drug tables in human
  example2 <- get_multimir(disease.drug='cisplatin', table='disease.drug')
  nrow(example2@data)
  head(example2@data)

---

List microRNAs, Genes, Drugs Or Diseases in the multiMiR Package

Description

list_multimir lists all the unique microRNAs, target genes, drugs, or diseases in the web server of the multiMiR package.

Usage

list_multimir(x = c("mirna", "gene", "drug", "disease"), limit = NULL,
  url = NULL)

list.multimir(x = c("mirna", "gene", "drug", "disease"), limit = NULL,
  url = NULL)

Arguments

x	a character string indicating what to list. This must be one of the strings "mirna" (default), "gene", "drug", or "disease". This can be abbreviated and is case insensitive.
limit	a positive integer. Limits the number of records returned from each table. Useful in testing potentially large queries.
url	Deprecated. Use global option multimir.url instead.

Details

list.multimir() has been deprecated and replaced with the list_multimir() version.

Value

list_multimir returns a data frame with information of microRNAs (microRNA unique ID, organism, mature microRNA accession number, and mature microRNA ID), target genes (gene unique ID, organism, gene symbol, Entrez gene ID, and Ensembl gene ID), drugs (drug names), and diseases (disease name).

Author(s)

Yuanbin Ru [email protected]

Examples

miRNAs <- list_multimir("mirna", limit = 10)
  genes <- list_multimir("gene", limit = 10)
  drugs <- list_multimir("drug", limit = 10)
  diseases <- list_multimir("disease", limit = 10)

---

S4 constructor and methods for object returned by get_multimir().

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

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.

---

MultiMiR: R package for accessing the multiMiR database

Description

This package provides an interface to the multiMiR database of microRNA-target interactions, and disease and drug associations. See http://multimir.org and the vignette ('multiMiR') for more details.

References

[Add reference here]

---

Collect Information About the Web Server And Database of the multiMiR Package

Description

Functions for collecting and displaying information about the web server and database of the multiMiR package.

Usage

multimir_dbInfo(url = NULL)

multimir_dbInfoVersions(url = NULL)

multimir_dbSchema(schema.file = NULL)

multimir_dbTables(url = NULL)

multimir_dbCount(url = NULL)

Arguments

url	Deprecated. Use global option multimir.url instead.
schema.file	Deprecated. Option exists as multimir.schema, but it should not need to be set directly.

Details

multimir.url is a global option containing the URL of the multiMiR web server. Set using options("multimir.url" = ...)

multimir_dbCount returns counts of records in the tables in the multiMiR database. Each table contains data from an external miRNA/target database.

multimir_dbInfo returns other information about the multiMiR database. This includes information of external miRNA/target databases in multiMiR.

multimir_dbInfoVersions returns other information about the multiMiR database versions available. This provides a list of available options if switching to previous version is desired.

multimir_dbSchema prints the schema definition of the multiMiR database.

multimir_dbTables returns the vector of tables in the multiMiR database and saves it to the global option multimir.tables.list. This function is automatically run when get_multimir is called if the multimir.tables.list is NULL.

Value

multimir_dbCount: a data frame with the count of records in each of the tables in the multiMiR database.

multimir_dbInfo: a data frame with information about the multiMiR database.

multimir_dbInfoVersions: a data frame with information about the multiMiR database versions.

multimir_dbSchema: none (invisible NULL).

multimir_dbTables: a data frame with table names in the multiMiR database.

Examples

this_url <- getOption("multimir.url")
  this_url
  options(multimir.url = this_url)
  
  db_ver <- multimir_dbInfoVersions()
  
  db_count <- multimir_dbCount()

  db_info <- multimir_dbInfo()

  multimir_dbSchema()

  db_tables <- multimir_dbTables()

---

Manage Database Version to use

Description

Functions for managing the database version used to complete requests on the web server.

Usage

multimir_switchDBVersion(db_version, url = NULL)

Arguments

db_version	A character string containing the full version number for the database version to use for for all package functions. The default will be the most recent version.
url	Deprecated. Use global option multimir.url instead.

Details

url is a character string containing the URL of the multiMiR web server. Optional as it is set when the package is loaded.

multimir_dbInfoVersions returns other information about the multiMiR database versions available. This provides a list of available options if switching to previous version is desired.

multimir_switchDBVersion returns other information about the multiMiR database versions available. This provides a list of available options if switching to previous version is desired.

Value

multimir_dbInfoVersions: a data frame with information about the multiMiR database versions.

multimir_switchDBVersion: none (invisible NULL).

Examples

multimir_dbInfoVersions()
  multimir_switchDBVersion(db_version="2.0.0")

---

Search the multiMiR Database Given a MySQL Query

Description

This is a function for directly querying the multiMiR database with MySQL queries. Given a MySQL query, it searches and retrieves result from the multiMiR database on the multiMiR web server. To use search_multimir directly, users will need to be familiar with MySQL and multiMiR table structures. Users are advised to use get_multimir instead.

Usage

search_multimir(query)

search.multimir(query)

Arguments

query

a character string for the MySQL query.

Details

search.multimir() has been deprecated and replaced with the search_multimir() version.

Value

search_multimir returns a data frame containing results from the multiMiR web server.

Examples

## show all tables in the multiMiR database
  tables <- search_multimir(query="show tables")

  ## show the structure of table diana_microt
  microt <- search_multimir(query="describe diana_microt")

  ## search for validated target genes of hsa-miR-18a-3p in miRecords
  qry <- paste("SELECT m.mature_mirna_acc, m.mature_mirna_id,",
               "    t.target_symbol, t.target_entrez, t.target_ensembl,",
               "    i.experiment, i.support_type, i.pubmed_id",
               "FROM mirna AS m INNER JOIN mirecords AS i INNER JOIN target",
               "AS t ON (m.mature_mirna_uid=i.mature_mirna_uid AND",
               "    i.target_uid=t.target_uid)",
               "WHERE m.mature_mirna_id='hsa-miR-18a-3p'")
  result <- search_multimir(query = qry)

---