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:
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`
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`