get_mir: Get microRNA correlations from cRegulome.db

Description Usage Arguments Value Examples

View source: R/get_data.R

Description

This function access the sqlite database file which is obtained by running get_db. Basically, the function provides ways to query the database to the correlation data of the microRNAs of interest. The function returns an error if the database file cRegulome.db is not in the working directory.

Usage

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get_mir(conn, mir, study, min_abs_cor, max_num, targets_only = FALSE)

Arguments

conn

A connection such as this returned by dbConnect

mir

A required character vector of the microRNAs of interest. These are the miRBase ID which are the official identifiers of the widely used miRBase database, http://www.mirbase.org/.

study

A character vector of The Cancer Genome Atlas (TCGA) study identifiers. To view the available studies in TCGA project, https://tcga-data.nci.nih.gov/docs/publications/tcga. When left to default NULL all available studies will be included.

min_abs_cor

A numeric, an absolute correlation minimum between 0 and 1 for each mir.

max_num

An integer, maximum number of features to show for each mir in each study.

targets_only

A logical, default FALSE. When TRUE, features will be the microRNA targets as defined in the package targetscan.Hs.eg.db.

Value

A tidy data.frame of four columns. mirna_base is the microRNA miRBase IDs, feature is the features/genes, cor is the corresponding expression correlations and study is TCGA study ID.

Examples

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# locate the testset file and connect
fl <- system.file('extdata', 'cRegulome.db', package = 'cRegulome')
conn <- RSQLite::dbConnect(RSQLite::SQLite(), fl)

# get microRNA correlations in all studies
get_mir(conn,
        mir = 'hsa-let-7g')

# get correlations in a particular study
get_mir(conn,
        mir = 'hsa-let-7g',
        study = 'STES')

# enter a custom query with different arguments
get_mir(conn,
        mir = 'hsa-let-7g',
        study = 'STES',
        min_abs_cor = .3,
        max_num = 5)

cRegulome documentation built on Sept. 21, 2018, 6:29 p.m.