Closed edoardopasolli closed 6 years ago
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
?
Yes! I was referring to the country field, but the same is true for the other ones
@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.
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.
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.
This issue was moved to waldronlab/curatedMetagenomicDataPipeline#2
it is missing what values correspond to. For example we should indicate that CAN=CANADA, DNK=Denmark, etc.