Minimum Required Columns for `topSNPs` File？

[laleoarrow]

Hello! Thank you for your fantastic work and contributions. I encountered a bit of confusion regarding the column requirements for the topSNPs file.

Problem Description

In the topSNPs example file, I noticed there are many columns, which makes it unclear which columns are strictly necessary. Could you clarify the minimum required columns for the topSNPs file? For example, would a file containing only significant lead SNPs or significant independent lead SNPs from FUMA be sufficient?

Desired Assistance

If possible, could you provide:

• A clear list of required vs. optional columns for the topSNPs file?
• Confirmation of whether files containing only significant lead SNPs or significant independent lead SNPs from FUMA would meet the requirements?

A simplified example of the topSNPs file format or a list of necessary columns with optional indicators would be incredibly helpful for setting up the data correctly.

Thank you very much for your time and assistance!

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[bschilder]

Apologies for the delayed response — this project is no longer funded and I am maintaining it in my free time.

Great question — and I've now added validation with clear error messages (commit 2d9b45b) so you get immediate feedback if columns are missing.

The minimum required columns for topSNPs are:

• Locus: Unique locus name (e.g., "TCF7L2")
• CHR: Chromosome (e.g., "12" or "chr12")
• POS (or BP): Genomic position in basepairs

Optional but helpful:

• SNP: Lead SNP RSID (if absent, assigned by min p-value)
• Gene: Gene name (used for labeling)

If any required columns are missing, you'll now get a clear error listing what's found vs required. A FUMA file should work if it has these columns. Use echodata::import_topSNPs() to standardize the format.

Please reopen if you need further help.