rnb.run.import {RnBeads} | R Documentation

## RnBeads Modules in the Analysis Pipeline

### Description

Functions that start the predefined modules in the RnBeads analysis pipeline.

### Usage

    rnb.run.import(data.source,
      data.type = rnb.getOption("import.default.data.type"), dir.reports,
      init.configuration = !file.exists(file.path(dir.reports, "configuration")),
      close.report = TRUE, show.report = FALSE)

    rnb.run.qc(rnb.set, dir.reports,
      init.configuration = !file.exists(file.path(dir.reports, "configuration")),
      close.report = TRUE, show.report = FALSE)

    rnb.run.preprocessing(rnb.set, dir.reports,
      init.configuration = !file.exists(file.path(dir.reports, "configuration")),
      close.report = TRUE, show.report = FALSE)

    rnb.run.inference(rnb.set, dir.reports,
      init.configuration = !file.exists(file.path(dir.reports, "configuration")),
      close.report = TRUE, show.report = FALSE)

    rnb.run.tnt(rnb.set, dir.reports,
      init.configuration = !file.exists(file.path(dir.reports, "configuration")),
      close.report = TRUE, show.report = FALSE)

    rnb.run.exploratory(rnb.set, dir.reports,
      init.configuration = !file.exists(file.path(dir.reports, "configuration")),
      close.report = TRUE, show.report = FALSE)

    rnb.run.differential(rnb.set, dir.reports,
      init.configuration = !file.exists(file.path(dir.reports, "configuration")),
      close.report = TRUE, show.report = FALSE)

### Arguments

`data.source` | `character` vector specifying the location of the data items on disk. The expected length of the vector differs for different values of `data.type`; see `rnb.execute.import` for a more detailed description.
`data.type` | `character` vector of length one specifying the type of the input data. The value of this parameter must be one of `"idat.dir"`, `"data.dir"`, `"data.files"`, `"GS.report"`, `"GEO"` or `"rnb.set"`. See `rnb.execute.import` for a more detailed description.
`dir.reports` | Directory to host the generated report file. Note that if this directory contains files, they may be overwritten.
`init.configuration` | Flag indicating if the configuration directory (usually shared among reports) should also be created.
`close.report` | Flag indicating if the created report is to be closed using the `off` method.
`show.report` | Flag indicating if the report is to be displayed after it is created. If this is, `TRUE` `rnb.show.report` is called to open the generated HTML file.
`rnb.set` | Methylation dataset as an object of type inheriting `RnBSet`.

### Details

The functions start the import, quality control, preprocessing, covariate inference, tracks and tables, exploratory analysis and differential methylation modules, respectively.

### Value

For `rnb.run.import`, `rnb.run.preprocessing` and `rnb.run.inference`, the returned value is a list of two elements - the initialized or modified dataset and the created report. All other functions return the created report, invisibly.

### Author(s)

Yassen Assenov

### See Also

`rnb.run.analysis` which executes these modules in the order given above

### Examples

    ### Running the modules step by step

    # Directory where your data is located
    data.dir <- "~/RnBeads/data/Ziller2011_PLoSGen_450K"
    idat.dir <- file.path(data.dir, "idat")
    sample.annotation <- file.path(data.dir, "sample_annotation.csv")

    # Directory where the output should be written to
    analysis.dir <- "~/RnBeads/analysis"
    # Directory where the report files should be written to
    report.dir <- file.path(analysis.dir, "reports_details")
    rnb.initialize.reports(report.dir)
    # Set some analysis options
    rnb.options(filtering.sex.chromosomes.removal = TRUE, identifiers.column = "Sample_ID")
    ## Restrict logging to the console only
    logger.start(fname = NA)

    ## Data import
    data.source <- c(idat.dir, sample.annotation)
    result <- rnb.run.import(data.source=data.source, data.type="idat.dir", dir.reports=report.dir)
    rnb.set <- result$rnb.set

    ## Quality Control
    rnb.run.qc(rnb.set, report.dir)

    ## Preprocessing
    rnb.set <- rnb.run.preprocessing(rnb.set, dir.reports=report.dir)$rnb.set

    ## Data export
    rnb.options(export.to.csv = TRUE)
    rnb.run.tnt(rnb.set, report.dir)

    ## Exploratory analysis
    rnb.run.exploratory(rnb.set, report.dir)

    ## Differential methylation
    rnb.run.differential(rnb.set, report.dir)

[Package RnBeads version 1.12.1 Index]