rnb.run.analysis {RnBeads} | R Documentation

## RnBeads Analysis Pipeline

### Description

Starts the RnBeads analysis pipeline on the given dataset. It loads the dataset if it is specified as a location.

### Usage

    rnb.run.analysis(dir.reports, data.source = NULL, sample.sheet = NULL,
      data.dir = NULL, GS.report = NULL, GEO.acc = NULL,
      data.type = rnb.getOption("import.default.data.type"),
      initialize.reports = TRUE, build.index = TRUE, save.rdata = TRUE)

### Arguments

`dir.reports` | Directory to host the generated report files. This must be a `character` of length one that specifies either a non-existent path (when `initialize.reports` is `TRUE`), or an existing directory (when `initialize.reports` is `FALSE`). In the latter case, a call to `rnb.initialize.reports` might be required before viewing the reports.
`data.source` | Methylation dataset as an object of type inheriting `RnBSet`, or a `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. If set, the parameters `sample.sheet`, `data.dir`, `GS.report`, `GEO.acc` will be ignored.
`sample.sheet` | A spreadsheet-like text file with sample annotations. The required columns are different for different values of `data.type`.
`data.dir` | For `data.type %in% c("data.dir", "idat.dir", "bed.dir")` a character singleton specifying the location of the directory with data files. The directory should have zero depth, i.e. should contain no subdirectories.
`GS.report` | GenomeStudio report file. `data.type` will be automatically set to `"GS.report"`.
`GEO.acc` | Gene Expression Omnibus accession of the data series with HumanMethylation450 data. `data.type` will be automatically set to `"GEO"`.
`data.type` | `character` vector of length one specifying the type of the input data. The value must be one of `"data.dir"`, `"idat.dir"`, `"GS.report"`, `"GEO"` or `"rnb.set"`. See `rnb.execute.import` for a more detailed description.
`initialize.reports` | Flag indicating if the report's directory must be initialized. If this parameter is set to `TRUE`, this function attempts to create the path specified by `dir.reports`. Otherwise, `dir.reports` is expected to signify an existing directory.
`build.index` | Flag indicating if a report index file (named `"index.html"`) should be created after all modules in the pipeline complete their analyses. If this is `TRUE`, the index file is also displayed using the function `rnb.show.report`.
`save.rdata` | Flag indicating whether important data objects (the filtered and unfiltered RnBSets, differential methylation) should be saved to an RData file in the reports folder.

### Value

Invisibly, the loaded, normalized and/or possibly filtered dataset as an object of type inheriting `RnBSet`.

### Author(s)

Yassen Assenov

### See Also

RnBeads modules

[Package RnBeads version 2.2.0 Index]