Package 'cRegulome' reference manual

Title:	Obtain and Visualize Regulome-Gene Expression Correlations in Cancer
Description:	Builds a 'SQLite' database file of pre-calculated transcription factor/microRNA-gene correlations (co-expression) in cancer from the Cistrome Cancer Liu et al. (2011) <doi:10.1186/gb-2011-12-8-r83> and 'miRCancerdb' databases (in press). Provides custom classes and functions to query, tidy and plot the correlation data.
Authors:	Mahmoud Ahmed [aut, cre]
Maintainer:	Mahmoud Ahmed <[email protected]>
License:	GPL-3
Version:	0.3.2
Built:	2024-08-19 05:54:50 UTC
Source:	https://github.com/ropensci/cRegulome

Construct cmicroRNA object

Description

Constructs an S3 object called cmicroRNA contains data returned by calling get_mir. Used to define methods for printing and visualizing microRNA-gene expression correlations.

Usage

cmicroRNA(dat_mir)
cmicroRNA(dat_mir)

Arguments

dat_mir

A data.frame such as this returned by calling get_mir.

Value

An S3 object of class cmicroRNA

Examples

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

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

# make a cmicroRNA object   
cmir <- cmicroRNA(dat)

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

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

# make a cmicroRNA object   
cmir <- cmicroRNA(dat)

A histogram of the correlations of microRNA or tf sets

Description

Plot a hist of sets of microRNAs or transcription factors-gene correlations in a TCGA study.

Usage

cor_hist(ob, study, ...)
cor_hist(ob, study, ...)

Arguments

`ob`	A cmicroRNA or cTF object such as this returned by calling cmicroRNA or cTF.
`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.
`...`	Other options

Value

An hist plot of the correlations values between genes a microRNA or a transcription factor in a TCGA study

Examples

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

# enter a custom query with different arguments
dat <- get_mir(conn,
               mir = c('hsa-let-7g', 'hsa-let-7i'),
               study = 'STES')

# make a cmicroRNA object   
cmir <- cmicroRNA(dat)

# print object
cor_hist(cmir)

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

# enter a custom query with different arguments
dat <- get_mir(conn,
               mir = c('hsa-let-7g', 'hsa-let-7i'),
               study = 'STES')

# make a cmicroRNA object   
cmir <- cmicroRNA(dat)

# print object
cor_hist(cmir)

Make an igraph object

Description

An igraph object of from cmicroRNA or cTF objects.

Usage

cor_igraph(ob, directed = FALSE)
cor_igraph(ob, directed = FALSE)

Arguments

`ob`	A cmicroRNA or cTF object such as this returned by calling cmicroRNA or cTF.
`directed`	A `logical` when `FALSE` the graph is indirected

Value

An igraph object

Examples

# load required libraries
library(RSQLite)
library(cRegulome)

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

# enter a custom query with different arguments
dat <- get_mir(conn,
               mir = c('hsa-let-7g', 'hsa-let-7i'),
               study = 'STES')

# make a cmicroRNA object   
cmir <- cmicroRNA(dat)

# print object
cor_igraph(cmir)

# load required libraries
library(RSQLite)
library(cRegulome)

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

# enter a custom query with different arguments
dat <- get_mir(conn,
               mir = c('hsa-let-7g', 'hsa-let-7i'),
               study = 'STES')

# make a cmicroRNA object   
cmir <- cmicroRNA(dat)

# print object
cor_igraph(cmir)

A joy plot of correlation of microRNA or tf sets

Description

A ggridges joy plot of sets of microRNAs or transcription factors-gene correlations in a TCGA study.

Usage

cor_joy(ob, study, ...)
cor_joy(ob, study, ...)

Arguments

`ob`	A cmicroRNA or cTF object such as this returned by calling cmicroRNA or cTF.
`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.
`...`	Other options

Value

An ggridges plot object

Examples

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

# enter a custom query with different arguments
dat <- get_mir(conn,
               mir = c('hsa-let-7g', 'hsa-let-7i'),
               study = 'STES')

# make a cmicroRNA object   
cmir <- cmicroRNA(dat)

# print object
cor_joy(cmir)

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

# enter a custom query with different arguments
dat <- get_mir(conn,
               mir = c('hsa-let-7g', 'hsa-let-7i'),
               study = 'STES')

# make a cmicroRNA object   
cmir <- cmicroRNA(dat)

# print object
cor_joy(cmir)

Plot method for cmicroRNA and cTF objects

Description

A dot plot of microRNA/TF correlation in a single study of TCGA. When the object cmicroRNA/cTF contains more than one TCGA studies, the argument study is a requirement.

Usage

cor_plot(ob, study, ...)
cor_plot(ob, study, ...)

Arguments

`ob`	A cmicroRNA or cTF object such as this returned by calling cmicroRNA or cTF.
`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.
`...`	Other options

Value

A ggplot object of a dot plot of the correlation values between genes and microRNAs or transcription factors in a TCGA study.

Examples

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

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

# make a cmicroRNA object   
cmir <- cmicroRNA(dat)

# print object
cor_plot(cmir)

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

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

# make a cmicroRNA object   
cmir <- cmicroRNA(dat)

# print object
cor_plot(cmir)

Prepare correlation data for plotting

Description

Not meant to be called directly by the user.

Usage

cor_prep(ob, study, add_dir = TRUE, add_corr = TRUE)
cor_prep(ob, study, add_dir = TRUE, add_corr = TRUE)

Arguments

`ob`	A cmicroRNA or cTF object such as this returned by calling cmicroRNA or cTF.
`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.
`add_dir`	A `logical` default TRUE for whether to add a column called Direction that has the direction of the correlation; positive or negative.
`add_corr`	A `logical` default TRUE for whether to add a column called Correlation that has the absolute value of the correlation

Value

A data.frame

Tidy cmicroRNA and cTF objects

Description

Tidy cmicroRNA and cTF objects

Usage

cor_tidy(ob)
cor_tidy(ob)

Arguments

`ob`	A cmicroRNA or cTF object such as this returned by calling cmicroRNA or cTF.

Value

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

Examples

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

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

# make a cmicroRNA object   
cmir <- cmicroRNA(dat)

# convert cmicroRNA object to a tidy data.frame
tidy_cmir <- cor_tidy(cmir)

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

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

# make a cmicroRNA object   
cmir <- cmicroRNA(dat)

# convert cmicroRNA object to a tidy data.frame
tidy_cmir <- cor_tidy(cmir)

`upset` plot of microRNA or tf sets

Description

upset of sets of microRNAs or transcription factors and their correlated features in a TCGA study.

Usage

cor_upset(ob, study, ...)
cor_upset(ob, study, ...)

Arguments

`ob`	A cmicroRNA or cTF object such as this returned by calling cmicroRNA or cTF.
`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.
`...`	Other options

Value

An upset plot

Examples

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

# enter a custom query with different arguments
dat <- get_mir(conn,
               mir = c('hsa-let-7g', 'hsa-let-7i'),
               study = 'STES')

# make a cmicroRNA object   
cmir <- cmicroRNA(dat)

# print object
cor_upset(cmir)

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

# enter a custom query with different arguments
dat <- get_mir(conn,
               mir = c('hsa-let-7g', 'hsa-let-7i'),
               study = 'STES')

# make a cmicroRNA object   
cmir <- cmicroRNA(dat)

# print object
cor_upset(cmir)

Venn Diagram of microRNA or transcription factor correlated features

Description

Count and plot the numbers of microRNA correlated features in cmicroRNA object.

Usage

cor_venn_diagram(ob, study, ...)
cor_venn_diagram(ob, study, ...)

Arguments

`ob`	A cmicroRNA or cTF object such as this returned by calling cmicroRNA or cTF.
`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.
`...`	Other options

Value

A venn diagram with a circle or an ellipses for each microRNA and the number of correlated features.

Examples

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

# enter a custom query with different arguments
dat <- get_mir(conn,
               mir = c('hsa-let-7g', 'hsa-let-7i'),
               study = 'STES')

# make a cmicroRNA object   
cmir <- cmicroRNA(dat)

# make graph
cor_venn_diagram(cmir)

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

# enter a custom query with different arguments
dat <- get_mir(conn,
               mir = c('hsa-let-7g', 'hsa-let-7i'),
               study = 'STES')

# make a cmicroRNA object   
cmir <- cmicroRNA(dat)

# make graph
cor_venn_diagram(cmir)

`cRegulome` package

Description

Download, access and visualize Regulome (microRNA and transcription factors) data from miRCancer and Cistrome cancer

Construct cTF object

Description

Constructs an S3 object called cTF contains data returned by calling get_tf. Used to define methods for printing and visualizing transcription factors-gene expression correlations.

Usage

cTF(dat_tf)
cTF(dat_tf)

Arguments

dat_tf

A data.frame such as this returned by calling get_tf.

Value

An S3 object of class cTF

Examples

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

# enter a custom query with different arguments
dat <- get_tf(conn,
              tf = 'LEF1',
              study = 'STES',
              min_abs_cor = .3,
              max_num = 5)

# make a cTF object   
ctf <- cTF(dat)

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

# enter a custom query with different arguments
dat <- get_tf(conn,
              tf = 'LEF1',
              study = 'STES',
              min_abs_cor = .3,
              max_num = 5)

# make a cTF object   
ctf <- cTF(dat)

This function calls download.file to download the pre-build database file of cRegulome. Additionally, the function checks the validity of the pre-defined URL and whether the database file exists in the current working directory to avoid redownloading it. Typically, users would run this function once at the first time the use the package or to update the database to the latest version.

Usage

get_db(test = FALSE, destfile, ...)
get_db(test = FALSE, destfile, ...)

Arguments

`test`	A `logical`, default `FALSE`. When `TRUE` downloads a database file with the same structure with a subset of the data for speed.
`destfile`	A character vector for the desired path for the database file. By default, when not specified, is constructed by using `tempdir` as a directory and the string `cRegulome.db.gz`
`...`	Optional arguments passed to `download.file`

Value

Downloads a compressed sqlite file to the current working directory. The file is named cRegulome.db.gz by default and it's not advised to change the name to avoid breaking the other functions that calls the database.

Examples

## Not run: 
# download a test set of the database
get_db(test = TRUE)

# download the full database file
get_db(test = FALSE)

## End(Not run)

# load the test db file from shipped with the pacakge
db_file <- system.file("extdata", "cRegulome.db", package = "cRegulome")
file.info(db_file)

## Not run: 
# download a test set of the database
get_db(test = TRUE)

# download the full database file
get_db(test = FALSE)

## End(Not run)

# load the test db file from shipped with the pacakge
db_file <- system.file("extdata", "cRegulome.db", package = "cRegulome")
file.info(db_file)

Get microRNA correlations from cRegulome.db

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

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

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` whether restrict the output to the recognized target features.
`targets`	A `character` vector of gene symbol names.

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

# 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)

# 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)

Get transcription factor correlations from cRegulome.db

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 transcription factors of interest. The function returns an error if the database file cRegulome.db is not in the working directory.

Usage

get_tf(conn, tf, study, min_abs_cor, max_num, targets_only = FALSE, targets)
get_tf(conn, tf, study, min_abs_cor, max_num, targets_only = FALSE, targets)

Arguments

`conn`	A connection such as this returned by `dbConnect`
`tf`	A required `character` vector of the transcription factor of interest. These are the HUGO official gene symbols of the genes contains the transcription factor.
`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` whether restrict the output to the recognized target features.
`targets`	A `character` vector of gene symbol names.

Value

A tidy data.frame of four columns. tf is the official gene symbols of the genes contains the transcription factor, feature is the features/genes, cor is the corresponding expression correlations and study is TCGA study ID.

Examples

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

## Not run: 
# get transcription factors correlations in all studies
get_tf(conn,
        tf = 'LEF1')

## End(Not run)

# get correlations in a particular study
get_tf(conn,
       tf = 'LEF1',
       study = 'STES')

# enter a custom query with different arguments
get_tf(conn,
       tf = 'LEF1',
       study = 'STES',
       min_abs_cor = .3,
       max_num = 5)

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

## Not run: 
# get transcription factors correlations in all studies
get_tf(conn,
        tf = 'LEF1')

## End(Not run)

# get correlations in a particular study
get_tf(conn,
       tf = 'LEF1',
       study = 'STES')

# enter a custom query with different arguments
get_tf(conn,
       tf = 'LEF1',
       study = 'STES',
       min_abs_cor = .3,
       max_num = 5)

Collect data from SQLite database

Description

Not meant to be called directly by the user.

Usage

stat_collect(conn, study, stat, type = "mir")
stat_collect(conn, study, stat, type = "mir")

Arguments

`conn`	A connection such as this returned by `dbConnect`
`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.
`stat`	A string such as this returned by `stat_make`
`type`	A `character` string. Either 'mir' of 'tf'. Used to define columns and tables names.

Value

A data.frame

Collect target features from SQLite database

Description

Not meant to be called directly by the user.

Usage

stat_collect_targets(conn, stat)
stat_collect_targets(conn, stat)

Arguments

`conn`	A connection such as this returned by `dbConnect`
`stat`	A string such as this returned by `stat_make`

Value

A character vector

Make A SQL statement

Description

Not meant to be called directly by the user.

Usage

stat_make(reg, study, min_abs_cor, max_num, targets, type = "mir")
stat_make(reg, study, min_abs_cor, max_num, targets, type = "mir")

Arguments

`reg`	A `character` vector of one or more regulator ID.
`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`	A `character` vector of gene symbol names.
`type`	A `character` string. Either 'mir' of 'tf'. Used to define columns and tables names.

Value

A character string

Examples

stat_make(reg = 'hsa-let-7g',
          study = 'STES')
          
stat_make(reg = 'hsa-let-7g',
          study = 'STES',
          min_abs_cor = .3)
          
stat_make(reg = 'hsa-let-7g',
          study = 'STES',
          min_abs_cor = .3,
          max_num = 5)
          
stat_make(reg = 'hsa-let-7g',
          study = 'STES')
          
stat_make(reg = 'hsa-let-7g',
          study = 'STES',
          min_abs_cor = .3)
          
stat_make(reg = 'hsa-let-7g',
          study = 'STES',
          min_abs_cor = .3,
          max_num = 5)

Make A SQL statement to extract target features

Description

Not meant to be called directly by the user.

Usage

stat_make_targets(reg, study, type = "mir")
stat_make_targets(reg, study, type = "mir")

Arguments

`reg`	A `character` vector of one or more regulator ID.
`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.
`type`	A `character` string. Either 'mir' of 'tf'. Used to define columns and tables names.

Value

A character string

Package 'cRegulome'

Help Index

Construct cmicroRNA object

Description

Usage

Arguments

Value

Examples

A histogram of the correlations of microRNA or tf sets

Description

Usage

Arguments

Value

Examples

Make an igraph object

Description

Usage

Arguments

Value

Examples

A joy plot of correlation of microRNA or tf sets

Description

Usage

Arguments

Value

Examples

Plot method for cmicroRNA and cTF objects

Description

Usage

Arguments

Value

Examples

Prepare correlation data for plotting

Description

Usage

Arguments

Value

Tidy cmicroRNA and cTF objects

Description

Usage

Arguments

Value

Examples

upset plot of microRNA or tf sets

Description

Usage

Arguments

Value

Examples

Venn Diagram of microRNA or transcription factor correlated features

Description

Usage

Arguments

Value

Examples

cRegulome package

Description

cRegulome functions to download and query the database file

cRegulome functions to create S3 objects

cRegulome functions to reshape S3 objects

cRegulome functions to visualize data in S3 objects

Construct cTF object

Description

Usage

Arguments

Value

Examples

Get cRegulome.db file

Description

Usage

Arguments

Value

Examples

Get microRNA correlations from cRegulome.db

Description

Usage

Arguments

Value

Examples

Get transcription factor correlations from cRegulome.db

`upset` plot of microRNA or tf sets

`cRegulome` package

`cRegulome` functions to download and query the database file

`cRegulome` functions to create S3 objects

`cRegulome` functions to reshape S3 objects

`cRegulome` functions to visualize data in S3 objects