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Additions and updates to documentation #16

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ossmith opened this issue Dec 17, 2024 · 0 comments
Open

Additions and updates to documentation #16

ossmith opened this issue Dec 17, 2024 · 0 comments
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documentation Improvements or additions to documentation

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@ossmith
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ossmith commented Dec 17, 2024

A few of the details in the documentation and arguments could benefit from clarification and consistency.

  • The naming schema is different between the two QuickStart commands (pgsus_height_example vs pegasus_height_decomposition), so they don't work together smoothly
  • --chrom-pos label for decomposition isn't defined (default behavior is unclear and causes unclear error). Seems like it should default to 'SNP' instead of 'chr.pos' since this is the output from/consistent with munge.
  • --bfile documentation doesn't clarify that this should just be the file stem (says 'bed file') and doesn't note what the default is
  • I think just including the name of the --anc-data file in the documentation would be good since it's non-obvious

Details around PRSice in munge:

  • Add PRSice as a dependency (or mention the conditions where it would be required) plus relevant instructions/pointer to install
  • Has this been tested with MacOS? PRSice_linux command is hardcoded as of now, so if there's no intent to add other OSs, I think it should just be noted in the documentation that this is only for Linux systems. (It's also a bit confusing since their instructions expect the command "PRSice")
@ossmith ossmith added the documentation Improvements or additions to documentation label Dec 17, 2024
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