Package 'BiasCorrector' reference manual

Title:	A GUI to Correct Measurement Bias in DNA Methylation Analyses
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>.
Authors:	Lorenz A. Kapsner [cre, aut, cph] , Evgeny A. Moskalev [aut]
Maintainer:	Lorenz A. Kapsner <[email protected]>
License:	GPL-3
Version:	0.2.3.9001
Built:	2024-11-16 06:22:01 UTC
Source:	https://github.com/kapsner/biascorrector

Launch BiasCorrector

Description

Launch BiasCorrector

Usage

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

if (interactive()) {
launch_app()
}

module_calibrationfile_server

Description

module_calibrationfile_server

Usage

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

Examples

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

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)
module_calibrationfile_ui(id)

Arguments

`id`	A character. The identifier of the shiny object

Value

The function returns a shiny ui module.

Examples

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

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, ...)
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.

Examples

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

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)
module_correctedplots_ui(id)

Arguments

`id`	A character. The identifier of the shiny object

Value

The function returns a shiny ui module.

Examples

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

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

module_correctedstatistics_ui

Description

module_correctedstatistics_ui

Usage

module_correctedstatistics_ui(id)
module_correctedstatistics_ui(id)

Arguments

`id`	A character. The identifier of the shiny object

Value

The function returns a shiny ui module.

Examples

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

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)
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.

Examples

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

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, ...)
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.

Examples

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

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)
module_experimentalfile_ui(id)

Arguments

`id`	A character. The identifier of the shiny object

Value

The function returns a shiny ui module.

Examples

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

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, ...)
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.

Examples

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

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, ...)
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.

Examples

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

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)
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.

Examples

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

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)
module_info_ui(id)

Arguments

`id`	A character. The identifier of the shiny object

Value

The function returns a shiny ui module.

Examples

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

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, ...)
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.

Examples

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

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)
module_log_ui(id)

Arguments

`id`	A character. The identifier of the shiny object

Value

The function returns a shiny ui module.

Examples

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

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)
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.

Examples

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

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)
module_modelselection_ui(id)

Arguments

`id`	A character. The identifier of the shiny object

Value

The function returns a shiny ui module.

Examples

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

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, ...)
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.

Examples

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

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)
module_plotting_ui(id)

Arguments

`id`	A character. The identifier of the shiny object

Value

The function returns a shiny ui module.

Examples

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

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, ...)
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.

Examples

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

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)
module_results_ui(id)

Arguments

`id`	A character. The identifier of the shiny object

Value

The function returns a shiny ui module.

Examples

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

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, ...)
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.

Examples

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

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)
module_settings_ui(id)

Arguments

`id`	A character. The identifier of the shiny object

Value

The function returns a shiny ui module.

Examples

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

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)
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.

Examples

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

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)
module_statistics_ui(id)

Arguments

`id`	A character. The identifier of the shiny object

Value

The function returns a shiny ui module.

Examples

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

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

Package 'BiasCorrector'

Help Index

Launch BiasCorrector

Description

Usage

Arguments

Value

Examples

module_calibrationfile_server

Description

Usage

Arguments

Value

See Also

Examples

module_calibrationfile_ui

Description

Usage

Arguments

Value

See Also

Examples

module_correctedplots_server

Description

Usage

Arguments

Value

See Also

Examples

module_correctedplots_ui

Description

Usage

Arguments

Value

See Also

Examples

module_correctedstatistics_ui

Description

Usage

Arguments

Value

See Also

Examples

module_correctedstats_server

Description

Usage

Arguments

Value

See Also

Examples

module_experimentalfile_server

Description

Usage

Arguments

Value

See Also

Examples

module_experimentalfile_ui

Description

Usage

Arguments

Value

See Also

Examples

module_fileupload_server

Description

Usage

Arguments

Value

See Also

Examples

module_fileupload_ui

Description

Usage

Arguments

Value

See Also

Examples

module_info_server

Description