Todo list for future milestone
This is to-do list for future milestone (the one that will come next, after conda packaging of ongoing valpha)
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current work is based on R 4.2. Move to R new version (4.3 or any updated version at time of novel milestone). That may require rewriting a bit the code, see https://cran.r-project.org/doc/manuals/r-release/NEWS.html -
move to r/qtl2 novel release (version 0.32), current work is based on qtl2 0.30. -
incorporate m39 (moving to qtl2 v 0.32 may turn helpful for parsing the sqlite, but overall this whole part needs to be rewritten in accordance with the display in interface to make it robust to both m38 and m39) -
add FDR as option for multiple testing, see issue #120 -
in code then interface, make recap table Peak start stop markers etc, see issue #89 -
Fix pmap/gmap use all across the code -
Fix filenames formatting for the peaks, refined regions, etc - no need to display in bp, poorly readable, think abt something new -
In refine regions, indexing to prune equivalent snps prior to top snps and/or asso