Comments (6)
I also think an interesting possibility would be to pool results from various tools here. Not exactly sure how to go about this at this stage.
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clumpak does something like that, although I haven't looked at it yet
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for admixture is this the change point in the CV graph?
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I think we can close this now, unless we want to put something in for Admixture?
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looks good. i'll add something in for admixture before closing that uses admixtures cross-validation method to select the min.
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I've added in admixture CV graph. Also throws error if the user hasn't added a log file.
With the repeated runs for STRUCTURE would it be possible to do something akin to https://en.wikipedia.org/wiki/Wilcoxon_signed-rank_test for model selection?
Also I don't know how mathematically sound this would be... but if you're doing repeated structure runs kinda akin to doing a 'bootstrap' like procedure ---> could do likelihood ratio tests?
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Related Issues (20)
- local shiny interface HOT 4
- print method for struct object
- reduce package size HOT 2
- clean up bestK function
- add phlyogentic trees to bar plots
- correlation metric for label switching problem
- test loadStructure output on other STRUCTURE models HOT 2
- inputs to functions should take struct, admix or Q matrix (either as lists or individually) HOT 2
- cody tidy up before release
- functions that make use of function from another library only once should be in suggests
- plot methods should return ggplot object
- Add in bootstrapping support for admixture HOT 1
- loadAdmixture fails on the log files if cv hasnt been run. HOT 1
- Clumpp needs to handle k=1 gracefully HOT 1
- bug: subsetting an admixList/structList/fastList to a single object returns a list
- populations parameter should be a character vector
- Loading multiple files at once HOT 2
- averagePairWiseSimilarityH
- loadStructure introducing NAs
- Cannot load structure output
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