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Dataset ID Doesn't Work for datasetID #11

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DarioS opened this issue Oct 29, 2024 · 2 comments
Open

Dataset ID Doesn't Work for datasetID #11

DarioS opened this issue Oct 29, 2024 · 2 comments

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@DarioS
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DarioS commented Oct 29, 2024

Creating a new Trio doesn't work if a dataset ID is specified to datasetID!

> datasets[1:3, 1:4]
# A tibble: 3 × 4
  datasetID name     source   sourceID         
  <chr>     <chr>    <chr>    <chr>            
1 0000      GE1_data figshare 26142922/47361037
2 0001      GE2_data figshare 26142922/47361052
3 0002      GE3_data figshare 26142922/47361049

> Trio$new("0001")
✔ Reading from Curated Trio Datasets.Range ''Datasets''.
Error in `private$parseIDString()`:
! Specified dataset ("0001") is not avaiable.

Only source ID works, despite

datasetID: A string specifying a dataset, either a name from curated-trio-data or a format string of the form source:source_id.

@nick-robo
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It's a little confusing, but the datasetID in Trio is the name in curated datasets. So to get dataset “0001”, you would give trio “GE1_data”.

Should I make the documentation clearer on this issue?

@DarioS
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DarioS commented Dec 4, 2024

Yes, names (e.g. gene names) are conventionally not unique, but IDs conventionally are. If the Trio class contructor's parameter name is datasetID I imagine that a lot of people would pick the datasetID column from the spreadsheet.

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