Title: A GUI to Correct Measurement Bias in DNA Methylation Analyses
Version: 0.2.3
Date: 2024-10-17
Description: A GUI to correct measurement bias in DNA methylation analyses. The 'BiasCorrector' package just wraps the functions implemented in the 'R' package 'rBiasCorrection' into a shiny web application in order to make them more easily accessible. Publication: Kapsner et al. (2021) <doi:10.1002/ijc.33681>.
License: GPL-3
URL: https://github.com/kapsner/BiasCorrector
BugReports: https://github.com/kapsner/BiasCorrector/issues
Depends: R (≥ 2.10)
Imports: data.table, DT, magrittr, rBiasCorrection (≥ 0.3.4), shiny, shinydashboard, shinyjs
Suggests: lintr, testthat
Encoding: UTF-8
NeedsCompilation: no
Packaged: 2024-10-17 14:21:58 UTC; user
Author: Lorenz A. Kapsner ORCID iD [cre, aut, cph], Evgeny A. Moskalev [aut]
Maintainer: Lorenz A. Kapsner <lorenz.kapsner@gmail.com>
Repository: CRAN
Date/Publication: 2024-10-17 14:40:02 UTC

Launch BiasCorrector

Description

Launch BiasCorrector

Usage

launch_app(
  port = 3838,
  plotdir = "plots",
  csvdir = "csv",
  logfilename = "biascorrector.log",
  maxfilesize = 100,
  parallel = TRUE
)

Arguments

port

The port, BiasCorrector is running on (default: 3838)

plotdir

A character string. Defaults to 'plots'. This directory is being created inside tempdir.

csvdir

A character string. Defaults to 'csv'. This directory is being created inside tempdir.

logfilename

A character string. The name of the logfile (default = biascorrector.log).

maxfilesize

A positive integer. The maximum file size allowed for upload.

parallel

A boolean. If TRUE (default), initializing 'future::plan("multiprocess")' before running the code.

Value

The function returns the BiasCorrector shiny application.

Examples

if (interactive()) {
launch_app()
}

module_calibrationfile_server

Description

module_calibrationfile_server

Usage

module_calibrationfile_server(input, output, session, rv, input_re, ...)

Arguments

input

Shiny server input object

output

Shiny server output object

session

Shiny session object

rv

The global 'reactiveValues()' object, defined in server.R

input_re

The Shiny server input object, wrapped into a reactive expression: input_re = reactive({input})

...

Further arguments, such as 'logfilename', 'csvdir' and 'plotdir'

Value

The function returns a shiny server module.

See Also

https://shiny.rstudio.com/articles/modules.html

Examples

if (interactive()) {
rv <- list()
logfilename <- paste0(tempdir(), "/log.txt")
shiny::callModule(
  module_calibrationfile_server,
  "moduleCalibrationFile",
  rv = rv,
  logfilename = logfilename
)
}

module_calibrationfile_ui

Description

module_calibrationfile_ui

Usage

module_calibrationfile_ui(id)

Arguments

id

A character. The identifier of the shiny object

Value

The function returns a shiny ui module.

See Also

https://shiny.rstudio.com/articles/modules.html

Examples

if (interactive()) {
shinydashboard::tabItems(
  shinydashboard::tabItem(
    tabName = "calibration",
    module_calibrationfile_ui(
      "moduleCalibrationFile"
    )
  )
)
}

module_correctedplots_server

Description

module_correctedplots_server

Usage

module_correctedplots_server(input, output, session, rv, input_re, ...)

Arguments

input

Shiny server input object

output

Shiny server output object

session

Shiny session object

rv

The global 'reactiveValues()' object, defined in server.R

input_re

The Shiny server input object, wrapped into a reactive expression: input_re = reactive({input})

...

Further arguments, such as 'logfilename', 'csvdir' and 'plotdir'

Value

The function returns a shiny server module.

See Also

https://shiny.rstudio.com/articles/modules.html

Examples

if (interactive()) {
rv <- list()
logfilename <- paste0(tempdir(), "/log.txt")
shiny::callModule(
  module_correctedplots_server,
  "moduleCorrectedPlots",
  rv = rv,
  logfilename = logfilename
)
}

module_correctedplots_ui

Description

module_correctedplots_ui

Usage

module_correctedplots_ui(id)

Arguments

id

A character. The identifier of the shiny object

Value

The function returns a shiny ui module.

See Also

https://shiny.rstudio.com/articles/modules.html

Examples

if (interactive()) {
shinydashboard::tabItems(
  shinydashboard::tabItem(
    tabName = "correctedplots",
    module_correctedplots_ui(
      "moduleCorrectedPlots"
    )
  )
)
}

module_correctedstatistics_ui

Description

module_correctedstatistics_ui

Usage

module_correctedstatistics_ui(id)

Arguments

id

A character. The identifier of the shiny object

Value

The function returns a shiny ui module.

See Also

https://shiny.rstudio.com/articles/modules.html

Examples

if (interactive()) {
shinydashboard::tabItems(
  shinydashboard::tabItem(
    tabName = "correctedstats",
    module_correctedstatistics_ui(
      "moduleCorrectedStats"
    )
  )
)
}

module_correctedstats_server

Description

module_correctedstats_server

Usage

module_correctedstats_server(input, output, session, rv, input_re)

Arguments

input

Shiny server input object

output

Shiny server output object

session

Shiny session object

rv

The global 'reactiveValues()' object, defined in server.R

input_re

The Shiny server input object, wrapped into a reactive expression: input_re = reactive({input})

Value

The function returns a shiny server module.

See Also

https://shiny.rstudio.com/articles/modules.html

Examples

if (interactive()) {
rv <- list()
logfilename <- paste0(tempdir(), "/log.txt")
shiny::callModule(
  module_correctedstats_server,
  "moduleCorrectedStats",
  rv = rv,
  logfilename = logfilename
)
}

module_experimentalfile_server

Description

module_experimentalfile_server

Usage

module_experimentalfile_server(input, output, session, rv, ...)

Arguments

input

Shiny server input object

output

Shiny server output object

session

Shiny session object

rv

The global 'reactiveValues()' object, defined in server.R

...

Further arguments, such as 'logfilename', 'csvdir' and 'plotdir'

Value

The function returns a shiny server module.

See Also

https://shiny.rstudio.com/articles/modules.html

Examples

if (interactive()) {
rv <- list()
logfilename <- paste0(tempdir(), "/log.txt")
shiny::callModule(
  module_experimentalfile_server,
  "moduleExperimentalFile",
  rv = rv,
  logfilename = logfilename
)
}

module_experimentalfile_ui

Description

module_experimentalfile_ui

Usage

module_experimentalfile_ui(id)

Arguments

id

A character. The identifier of the shiny object

Value

The function returns a shiny ui module.

See Also

https://shiny.rstudio.com/articles/modules.html

Examples

if (interactive()) {
shinydashboard::tabItems(
  shinydashboard::tabItem(
    tabName = "experimental",
    module_experimentalfile_ui(
      "moduleExperimentalFile"
    )
  )
)
}

module_fileupload_server

Description

module_fileupload_server

Usage

module_fileupload_server(input, output, session, rv, input_re, ...)

Arguments

input

Shiny server input object

output

Shiny server output object

session

Shiny session object

rv

The global 'reactiveValues()' object, defined in server.R

input_re

The Shiny server input object, wrapped into a reactive expression: input_re = reactive({input})

...

Further arguments, such as 'logfilename', 'csvdir' and 'plotdir'

Value

The function returns a shiny server module.

See Also

https://shiny.rstudio.com/articles/modules.html

Examples

if (interactive()) {
rv <- list()
logfilename <- paste0(tempdir(), "/log.txt")
shiny::callModule(
  module_fileupload_server,
  "moduleEileUpload",
  rv = rv,
  logfilename = logfilename
)
}

module_fileupload_ui

Description

module_fileupload_ui

Usage

module_fileupload_ui(id, ...)

Arguments

id

A character. The identifier of the shiny object

...

Further arguments, such as 'maxfilesize'

Value

The function returns a shiny ui module.

See Also

https://shiny.rstudio.com/articles/modules.html

Examples

if (interactive()) {
shinydashboard::tabItems(
  shinydashboard::tabItem(
    tabName = "fileupload",
    module_fileupload_ui(
      "moduleFileUpload",
      maxfilesize = maxfilesize
    )
  )
)
}

module_info_server

Description

module_info_server

Usage

module_info_server(input, output, session, rv, input_re)

Arguments

input

Shiny server input object

output

Shiny server output object

session

Shiny session object

rv

The global 'reactiveValues()' object, defined in server.R

input_re

The Shiny server input object, wrapped into a reactive expression: input_re = reactive({input})

Value

The function returns a shiny server module.

See Also

https://shiny.rstudio.com/articles/modules.html

Examples

if (interactive()) {
rv <- list()
logfilename <- paste0(tempdir(), "/log.txt")
shiny::callModule(
  module_info_server,
  "moduleInfo",
  rv = rv,
  logfilename = logfilename
)
}

module_info_ui

Description

module_info_ui

Usage

module_info_ui(id)

Arguments

id

A character. The identifier of the shiny object

Value

The function returns a shiny ui module.

See Also

https://shiny.rstudio.com/articles/modules.html

Examples

if (interactive()) {
shinydashboard::tabItems(
  shinydashboard::tabItem(
    tabName = "info",
    module_info_ui(
      "moduleInfo"
    )
  )
)
}

module_log_server

Description

module_log_server

Usage

module_log_server(input, output, session, rv, input_re, ...)

Arguments

input

Shiny server input object

output

Shiny server output object

session

Shiny session object

rv

The global 'reactiveValues()' object, defined in server.R

input_re

The Shiny server input object, wrapped into a reactive expression: input_re = reactive({input})

...

Further arguments, such as 'logfilename', 'csvdir' and 'plotdir'

Value

The function returns a shiny server module.

See Also

https://shiny.rstudio.com/articles/modules.html

Examples

if (interactive()) {
rv <- list()
logfilename <- paste0(tempdir(), "/log.txt")
shiny::callModule(
  module_log_server,
  "moduleLog",
  rv = rv,
  logfilename = logfilename
)
}

module_log_ui

Description

module_log_ui

Usage

module_log_ui(id)

Arguments

id

A character. The identifier of the shiny object

Value

The function returns a shiny ui module.

See Also

https://shiny.rstudio.com/articles/modules.html

Examples

if (interactive()) {
shinydashboard::tabItems(
  shinydashboard::tabItem(
    tabName = "log",
    module_log_ui(
      "moduleLog"
    )
  )
)
}

module_modelselection_server

Description

module_modelselection_server

Usage

module_modelselection_server(input, output, session, rv, input_re)

Arguments

input

Shiny server input object

output

Shiny server output object

session

Shiny session object

rv

The global 'reactiveValues()' object, defined in server.R

input_re

The Shiny server input object, wrapped into a reactive expression: input_re = reactive({input})

Value

The function returns a shiny server module.

See Also

https://shiny.rstudio.com/articles/modules.html

Examples

if (interactive()) {
rv <- list()
logfilename <- paste0(tempdir(), "/log.txt")
shiny::callModule(
  module_modelselection_server,
  "moduleModelSelection",
  rv = rv,
  logfilename = logfilename
)
}

module_modelselection_ui

Description

module_modelselection_ui

Usage

module_modelselection_ui(id)

Arguments

id

A character. The identifier of the shiny object

Value

The function returns a shiny ui module.

See Also

https://shiny.rstudio.com/articles/modules.html

Examples

if (interactive()) {
shinydashboard::tabItems(
  shinydashboard::tabItem(
    tabName = "modelselection",
    module_modelselection_ui(
      "moduleModelSelection"
    )
  )
)
}

module_plotting_server

Description

module_plotting_server

Usage

module_plotting_server(input, output, session, rv, input_re, ...)

Arguments

input

Shiny server input object

output

Shiny server output object

session

Shiny session object

rv

The global 'reactiveValues()' object, defined in server.R

input_re

The Shiny server input object, wrapped into a reactive expression: input_re = reactive({input})

...

Further arguments, such as 'logfilename', 'csvdir' and 'plotdir'

Value

The function returns a shiny server module.

See Also

https://shiny.rstudio.com/articles/modules.html

Examples

if (interactive()) {
rv <- list()
logfilename <- paste0(tempdir(), "/log.txt")
shiny::callModule(
  module_plotting_server,
  "modulePlotting",
  rv = rv,
  logfilename = logfilename
)
}

module_plotting_ui

Description

module_plotting_ui

Usage

module_plotting_ui(id)

Arguments

id

A character. The identifier of the shiny object

Value

The function returns a shiny ui module.

See Also

https://shiny.rstudio.com/articles/modules.html

Examples

if (interactive()) {
shinydashboard::tabItems(
  shinydashboard::tabItem(
    tabName = "plotting",
    module_plotting_ui(
      "modulePlotting"
    )
  )
)
}

module_results_server

Description

module_results_server

Usage

module_results_server(input, output, session, rv, input_re, ...)

Arguments

input

Shiny server input object

output

Shiny server output object

session

Shiny session object

rv

The global 'reactiveValues()' object, defined in server.R

input_re

The Shiny server input object, wrapped into a reactive expression: input_re = reactive({input})

...

Further arguments, such as 'logfilename', 'csvdir' and 'plotdir'

Value

The function returns a shiny server module.

See Also

https://shiny.rstudio.com/articles/modules.html

Examples

if (interactive()) {
rv <- list()
logfilename <- paste0(tempdir(), "/log.txt")
shiny::callModule(
  module_results_server,
  "moduleResults",
  rv = rv,
  logfilename = logfilename
)
}

module_results_ui

Description

module_results_ui

Usage

module_results_ui(id)

Arguments

id

A character. The identifier of the shiny object

Value

The function returns a shiny ui module.

See Also

https://shiny.rstudio.com/articles/modules.html

Examples

if (interactive()) {
shinydashboard::tabItems(
  shinydashboard::tabItem(
    tabName = "results",
    module_results_ui(
      "moduleResults"
    )
  )
)
}

module_settings_server

Description

module_settings_server

Usage

module_settings_server(input, output, session, rv, input_re, ...)

Arguments

input

Shiny server input object

output

Shiny server output object

session

Shiny session object

rv

The global 'reactiveValues()' object, defined in server.R

input_re

The Shiny server input object, wrapped into a reactive expression: input_re = reactive({input})

...

Further arguments, such as 'logfilename', 'csvdir' and 'plotdir'

Value

The function returns a shiny server module.

See Also

https://shiny.rstudio.com/articles/modules.html

Examples

if (interactive()) {
rv <- list()
logfilename <- paste0(tempdir(), "/log.txt")
shiny::callModule(
  module_settings_server,
  "moduleSettings",
  rv = rv,
  logfilename = logfilename
)
}

module_settings_ui

Description

module_settings_ui

Usage

module_settings_ui(id)

Arguments

id

A character. The identifier of the shiny object

Value

The function returns a shiny ui module.

See Also

https://shiny.rstudio.com/articles/modules.html

Examples

if (interactive()) {
shinydashboard::tabItems(
  shinydashboard::tabItem(
    tabName = "settings",
    module_settings_ui(
      "moduleSettings"
    )
  )
)
}

module_statistics_server

Description

module_statistics_server

Usage

module_statistics_server(input, output, session, rv, input_re)

Arguments

input

Shiny server input object

output

Shiny server output object

session

Shiny session object

rv

The global 'reactiveValues()' object, defined in server.R

input_re

The Shiny server input object, wrapped into a reactive expression: input_re = reactive({input})

Value

The function returns a shiny server module.

See Also

https://shiny.rstudio.com/articles/modules.html

Examples

if (interactive()) {
rv <- list()
logfilename <- paste0(tempdir(), "/log.txt")
shiny::callModule(
  module_statistics_server,
  "moduleStatistics",
  rv = rv,
  logfilename = logfilename
)
}

module_statistics_ui

Description

module_statistics_ui

Usage

module_statistics_ui(id)

Arguments

id

A character. The identifier of the shiny object

Value

The function returns a shiny ui module.

See Also

https://shiny.rstudio.com/articles/modules.html

Examples

if (interactive()) {
shinydashboard::tabItems(
  shinydashboard::tabItem(
    tabName = "statistics",
    module_statistics_ui(
      "moduleStatistics"
    )
  )
)
}