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1. When a sparse GRM is used to fit the null model (--useSparseGRMtoFitNULL=TRUE)
* Multiple variance ratios need to be estimated based on different minor allele count categories with *--isCateVarianceRatio=TRUE*** Different from Step 1 in SAIGE for single-variant tests in SAIGE, in which only a single variance ratio is estiamted
** By default, two variance ratios are estiamted for 10 <= MAC < 20 and MAC >= 20.
However, the two-star inner bullet points are not a valid syntax for a markdown file, which results in these sections failing to render properly in the html: https://saigegit.github.io/SAIGE-doc/docs/set_step1.html
I suspect removing the second asterisk from each of these lines would solve the problem.
Relatedly, *--isCateVarianceRatio=TRUE* condenses the double-dash into an emdash--it would be better to put this into an inline code block, like such: [...]`--isCateVarianceRatio=TRUE`
The text was updated successfully, but these errors were encountered:
In a number of places in the documentation, you seem to be trying to make multi-level bulleted lists. e.g. in https://raw.githubusercontent.com/saigegit/SAIGE-doc/saige-pages/docs/set_step1.md:
However, the two-star inner bullet points are not a valid syntax for a markdown file, which results in these sections failing to render properly in the html:
https://saigegit.github.io/SAIGE-doc/docs/set_step1.html
I suspect removing the second asterisk from each of these lines would solve the problem.
Relatedly,
*--isCateVarianceRatio=TRUE*
condenses the double-dash into an emdash--it would be better to put this into an inline code block, like such:[...]`--isCateVarianceRatio=TRUE`
The text was updated successfully, but these errors were encountered: