rnb.execute.export.csv

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Description

Exports (selected) methylation tables of the given dataset to comma-separated value files.

Usage

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rnb.execute.export.csv(rnb.set, output.location,
  region.types = rnb.getOption("export.types"))

Arguments

rnb.set

Methylation dataset as an object of type inheriting RnBSet.

output.location

character or Report specifying the output directory. If this is a report, the output directory is set to be a subdirectory named csv of the report's data directory. Set this parameter to the empty string ("") or NA to use the current working directory. If the given path does not exist, this function attempts to create it.

region.types

character vector indicating region types to be exported.

Details

The names of the generated output files are formed by the prefix "betas_", followed by a number between 1 and length(region.types). The extension is .csv or .csv.gz, depending on the value of the RnBeads option "gz.large.files". Any such files that already exist in the output directory, are overwritten.

There are several reasons why a certain output file cannot be (fully) generated. Examples for failures are listed below:

  • The corresponding region type is invalid.

  • The corresponding region type is not supported by the dataset. If the type is loaded in RnBeads, use the summarize.regions method prior to calling this function, in order to include the support of this region type in the dataset.

  • Due to security restrictions, the creation of files in the output directory is not allowed.

  • A file or directory with the same name exists and cannot be overwritten.

  • The disk is full or the user quota is exceeded.

Value

character vector containing the names of the files to which data were exported; prepended by output.location. In case a certain region type could not be exported (see the Details section), the corresponding element of this vector is NA.

Author(s)

Yassen Assenov

Examples

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library(RnBeads.hg19)
data(small.example.object)
rnb.execute.export.csv(rnb.set.example, "", summarized.regions(rnb.set.example))

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