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feat: iterative approach #47

Merged
merged 41 commits into from
Dec 5, 2024
Merged

feat: iterative approach #47

merged 41 commits into from
Dec 5, 2024

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aryarm
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@aryarm aryarm commented Dec 5, 2024

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aryarm added 30 commits September 25, 2024 13:47
@aryarm
create first iteration of forest builder
b420ee2
@aryarm
use new config file for simulations
c937bb6
@aryarm
use new --max-signals param in happler
0bcf1b2
@aryarm
make simulate workflow reproducible
7a84684
@aryarm
output multiple haps in choose_different_ld
0431d4b
@aryarm
try (and fail) to import graphviz trees
c1dbe5b 
TODO: fix this later
@aryarm
simply output an empty file when all haps are SNPs
7a589bb
@aryarm
enable graphviz output for multiple trees
51766a5
@aryarm
simulate multiple haps as well
7cd90cb
@aryarm
match obs and causal haps by their LD
35eded4
@aryarm
implement a final haplotype threshold too
f28dda5
@aryarm
color each point of the parameter plot by whether it is an extra
635079e
@aryarm
enable simulation replicates
c89f6e5
@aryarm
output finemapping metrics for multiple haps
8070c4e
@aryarm
allow for setting output threshold as a param in the config
4edfd01
@aryarm
clean up and update scripts README
8371c80
@aryarm
handle empty hap files in utils.R
1b5a9ed
@aryarm
allow for reordering rows of parameter_plot
c8e2eb5
@aryarm
allow for leniency when estimating pvals in happler
4f5b24b
@aryarm
make thresh more lenient
46fe5ca
@aryarm
split pheno for happler rules
1584890
@aryarm
set up workflow for running on geuvadis again
63bd60b
@aryarm
switch to geuvadis config
eeb4659
@aryarm
enable pickling as a parameter plot option
1dbe559
@aryarm
start to try to handle multiple haps in summarize_results.R
4383e3f
@aryarm
enable computing mean and stderr of finemapping metrics in parameter_…
23735cf 
…plot
@aryarm
adjust the amount of time for the multiline rule
b9a1c22
@aryarm
start on STR analysis
e1f01c3
@aryarm
revert to min for now. need to come up with a better way of doing thi…
321ced6 
…s eventually
@aryarm
allow for pickled output for explained_variances.png
f0b5b38
@aryarm aryarm merged commit 3090781 into feat/ukb Dec 5, 2024
7 of 10 checks passed
@aryarm aryarm deleted the feat/forests branch December 5, 2024 22:04
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