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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")
The text was updated successfully, but these errors were encountered:
A few of the details in the documentation and arguments could benefit from clarification and consistency.
pgsus_height_example
vspegasus_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--anc-data
file in the documentation would be good since it's non-obviousDetails around PRSice in munge:
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")The text was updated successfully, but these errors were encountered: