country

[edoardopasolli]

it is missing what values correspond to. For example we should indicate that CAN=CANADA, DNK=Denmark, etc.

[lwaldron]

The description column in inst/extdata/template.csv says:

Country of acquisition using ISO3 code from http://www.fao.org/countryprofiles/iso3list/en/

Is the issue more that these descriptions do not make it to pData or combined_metadata?

[edoardopasolli]

Yes! I was referring to the country field, but the same is true for the other ones

[lwaldron]

@schifferl would you add these descriptions to the metadata of the ExpressionSets and the combined_metadata? For the esets, it's varMetadata(); for example:

> example("ExpressionSet")
> varMetadata(expressionSet)
      labelDescription
sex        Female/Male
type      Case/Control
score    Testing Score

If combined_metadata were a DataFrame, it would be in metadata(combined_metadata), but I don't know what the options are for a tbl_df. I would probably suggest going the "Bioconductor way" and using a DataFrame which has metadata in a place many users will expect.

Metadata should be mentioned in the man pages and vignette.

[schifferl]

Ok, I will convert the combined_metadata to a DataFrame and add the descriptions. I agree too, the metadata should be mentioned in the ?curatedMetagenomicData man page and perhaps even have it's own man page.

[lwaldron]

I'd say ?curatedMetagenomicData could just explain what is provided by the important accessors of the ExpressionSet objects (exprs, pData, varMetadata, rownames, colnames, plus the six data products), and also mention the other key components of the package: conversion to phyloseq and metagenomeSeq, and the combined_metadata table, with these listed under See Also). Then the metadata can be documented under ?combined_metadata and in the vignette.

[schifferl]

This issue was moved to waldronlab/curatedMetagenomicDataPipeline#2