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epigen / RnBeads

Git working Repo synced to the Bioconductor: http://bioconductor.org/packages/devel/bioc/html/RnBeads.html
https://rnbeads.org/
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Minor issue in docs related to import #6

Closed markziemann closed 3 years ago

markziemann commented 4 years ago

https://github.com/epigen/RnBeads/blob/32939a6014a6dd8d15a60c3afd95d4f924a7e5db/vignettes/RnBeads.Rnw#L446 It looks like c() is not working as expected and should be changed with list() or other?

> res <- rnb.run.import(dir.reports=report.dir, data.source=c(idat.dir,sample.annotation),  data.type="infinium.idat.dir")
2020-01-23 12:05:58     1.5  STATUS                             STARTED Loading Data
2020-01-23 12:05:58     1.5    INFO                                 Number of cores: 1
2020-01-23 12:05:58     1.5    INFO                                 Loading data of type "infinium.idat.dir"
2020-01-23 12:05:58     1.5   ERROR                                 invalid data.source parameter, sample annotation file not found, or is a directory
Error in logger.error(txt) : 
  invalid data.source parameter, sample annotation file not found, or is a directory
> res <- rnb.run.import(dir.reports=report.dir, data.source=list(idat.dir,sample.annotation),  data.type="infinium.idat.dir")
2020-01-23 12:06:09     1.5  STATUS                                 STARTED Loading Data
2020-01-23 12:06:10     1.5    INFO                                     Number of cores: 1
2020-01-23 12:06:10     1.5    INFO                                     Loading data of type "infinium.idat.dir"
2020-01-23 12:06:10     1.5  STATUS                                     STARTED Loading Data from IDAT Files
2020-01-23 12:06:10     1.5    INFO                                         Added column barcode to the provided sample annotation table
2020-01-23 12:06:10     1.5    INFO                                         Detected platform: MethylationEPIC
2020-01-23 12:08:29     2.0  STATUS                                     COMPLETED Loading Data from IDAT Files