Bioconductor Code: epistasisGA

Graph of epistasisGA

8fc478c (HEAD -> devel, origin/devel, origin/HEAD) address minor warnings and update documentation by mnodzenski <[email protected]> 2025-07-14 22:37:57 -0400;
94dbf1e bump version number to build E-GADGETS update by mnodzenski <[email protected]> 2025-07-06 14:40:40 -0400;
72dee36 Updated version of E-GADGETS with new nomination procedure for risk alleles and permuting exposure in the standardization step. by mnodzenski <[email protected]> 2023-02-15 16:00:27 -0500;
5646bd1 Merge pull request <a href="#2">#2</a> from SciomeLLC/dev by Michael Nodzenski <[email protected]> 2025-07-06 13:24:12 -0400;
0c88feb bump x.y.z version to odd y following creation of RELEASE_3_21 branch by A Wokaty <[email protected]> 2025-04-15 12:57:09 -0400;
6b37aae (origin/RELEASE_3_21, RELEASE_3_21) bump x.y.z version to even y prior to creation of RELEASE_3_21 branch by A Wokaty <[email protected]> 2025-04-15 12:57:09 -0400;
a8c940b (origin/master) bump x.y.z version to odd y following creation of RELEASE_3_20 branch by J Wokaty <[email protected]> 2024-10-29 11:14:56 -0400;
8a85b57 (origin/RELEASE_3_20, RELEASE_3_20) bump x.y.z version to even y prior to creation of RELEASE_3_20 branch by J Wokaty <[email protected]> 2024-10-29 11:14:55 -0400;
aed48a4 Merge branch 'master' of github-sciome-bot:SciomeLLC/epistasisGA into dev by sciome-bot <[email protected]> 2024-06-25 16:23:40 -0400;
8246307 fixing bug in missing data preprocessing by sciome-bot <[email protected]> 2024-06-25 16:22:53 -0400;
2374862 bump x.y.z version to odd y following creation of RELEASE_3_19 branch by J Wokaty <[email protected]> 2024-04-30 11:45:06 -0400;
56191c1 (origin/RELEASE_3_19, RELEASE_3_19) bump x.y.z version to even y prior to creation of RELEASE_3_19 branch by J Wokaty <[email protected]> 2024-04-30 11:45:06 -0400;
5481a6e Modifying vignette to clarify global permutation tests vs. not. fleshing out information on SNPs in the same LD block. by sciome-bot <[email protected]> 2024-03-27 10:28:27 -0400;
47b4d30 Final change to markdown -- change from David and Clare by Taylor Petty <[email protected]> 2024-03-15 11:54:22 -0400;
bbb85cb remove explanation of why external data, per David's suggestion by Taylor Petty <[email protected]> 2024-03-13 16:29:31 -0400;
1696b9f Minor additions from Clare by Taylor Petty <[email protected]> 2024-03-13 11:38:17 -0400;
026fe9f fleshing out information on SNPs in the same LD block by Taylor Petty <[email protected]> 2024-03-12 15:03:57 -0400;
93eb8f0 Modifying vignette to clarify global permutation tests vs. not by Taylor Petty <[email protected]> 2024-03-12 13:23:03 -0400;
08dc0f6 bump x.y.z version to odd y following creation of RELEASE_3_18 branch by J Wokaty <[email protected]> 2023-10-24 11:44:31 -0400;
a4f5fdc (origin/RELEASE_3_18, RELEASE_3_18) bump x.y.z version to even y prior to creation of RELEASE_3_18 branch by J Wokaty <[email protected]> 2023-10-24 11:44:31 -0400;
48703f2 (origin/RELEASE_3_17, RELEASE_3_17) Bump version to trigger rebuild and propagation of new Mac binary by J Wokaty <[email protected]> 2023-05-01 20:10:26 -0400;
11497c1 bump x.y.z version to odd y following creation of RELEASE_3_17 branch by J Wokaty <[email protected]> 2023-04-25 11:40:34 -0400;
4f2f4b9 bump x.y.z version to even y prior to creation of RELEASE_3_17 branch by J Wokaty <[email protected]> 2023-04-25 11:40:34 -0400;
89c2598 (origin/RELEASE_3_16, RELEASE_3_16) Bump version to trigger rebuild and propagation of new Mac binary by J Wokaty <[email protected]> 2023-01-19 11:16:58 -0500;
e497130 Yet another try to get preprocessing function to work on windows, now by explictly removing the objects when done running gc prior to unlinking temp files by mnodzenski <[email protected]> 2023-01-10 13:44:57 -0500;
2ce6cee Another try at making this work on windows, now by explicitly attaching big.matrix files in bplapply by mnodzenski <[email protected]> 2023-01-09 12:44:30 -0500;
6824d43 Trying to fix build issue on windows and warning on linux. by mnodzenski <[email protected]> 2023-01-06 14:36:40 -0500;
7826cb1 Update two new vignettes. by mnodzenski <[email protected]> 2023-01-04 12:18:13 -0500;
acc6442 Go back to version 1.1.1 to correctly increment the devel branch by mnodzenski <[email protected]> 2023-01-04 10:02:13 -0500;
6f93f63 Update E-GADGETS vignette based on updated fitness score by mnodzenski <[email protected]> 2022-12-28 14:34:22 -0500;
35a876a Make sure we report the correct intercept by mnodzenski <[email protected]> 2022-12-27 18:08:38 -0500;
0e49df8 Trying a third version of the E-GADGETS fitness score. by mnodzenski <[email protected]> 2022-12-14 10:08:05 -0500;
808b4e7 Bump version to trigger rebuild and propagation of new arm64 binary by J Wokaty <[email protected]> 2022-12-13 18:06:25 -0500;
5cf3afb Updating E-GADGETS with new parent-based component instead of allelic heterogeneity. by mnodzenski <[email protected]> 2022-12-09 10:45:01 -0500;
26548a6 Further edits in preparation for propagating E-GADGETS and maternal-fetal effects to bionconductor. by mnodzenski <[email protected]> 2022-11-24 08:01:34 -0500;
c7445cf Merging in original epistasisGA package by mnodzenski <[email protected]> 2022-11-22 16:35:09 -0500;
c60ab14 Preparing to merge in with original epistasisGA package. by mnodzenski <[email protected]> 2022-11-22 13:45:46 -0500;
1854b8f For now, make maternal_fetal_adj back compatible, even though it won't be used. by mnodzenski <[email protected]> 2022-11-15 14:43:37 -0500;
d7f38b1 Adding in new vignettes. by mnodzenski <[email protected]> 2022-11-11 15:35:01 -0500;
ab9f0fd Adding in functions to turn off the matenral-fetal adjustment and to test specifically for maternal-fetal interaction with the epsitasis test. by mnodzenski <[email protected]> 2022-11-07 11:18:47 -0500;
5267630 bump x.y.z version to odd y following creation of RELEASE_3_16 branch by J Wokaty <[email protected]> 2022-11-01 11:27:38 -0400;
e1353aa bump x.y.z version to even y prior to creation of RELEASE_3_16 branch by J Wokaty <[email protected]> 2022-11-01 11:27:38 -0400;
c315809 Actually do need the family-based fitness component so switch back to using it by default by mnodzenski <[email protected]> 2022-10-27 09:31:54 -0400;
2f41e63 Adding in E-GADGETS vignette and fixing the on-off switch for the family-based E-GADGET component by mnodzenski <[email protected]> 2022-10-26 13:04:35 -0400;
1eff981 Moving in the direction of merging this with the bioconductor package. by mnodzenski <[email protected]> 2022-10-26 08:53:11 -0400;
78a7f63 updating to fix build issue on windows by mnodzenski <[email protected]> 2022-10-19 15:22:03 -0400;
bad6c7f Don't compute correlation between mom and child SNPs by mnodzenski <[email protected]> 2022-09-27 13:03:21 -0400;
76d9e2b Make sure n chroms is right when using GxE function by mnodzenski <[email protected]> 2022-09-26 12:03:41 -0400;
cb21f60 Make clear that, for permutes, we need to specify the original mean.vec and sd.vec by mnodzenski <[email protected]> 2022-09-07 10:04:33 -0400;
41f32ff Fix edge cases for GxE fitness score by mnodzenski <[email protected]> 2022-08-22 11:03:02 -0400;
b6941a0 update gitignore by mnodzenski <[email protected]> 2022-08-22 10:58:17 -0400;
28a215e Turn off shared memory usage for as.big.matrix by mnodzenski <[email protected]> 2022-08-21 10:11:02 -0400;
130351a Make permute function work for exposures by mnodzenski <[email protected]> 2022-08-21 09:47:52 -0400;
8d2acd7 fix compiler warning by adding parantheses by mnodzenski <[email protected]> 2022-08-09 17:12:21 -0400;
6081892 bumping version to rebuild after subscribing to bioc devel list by mnodzenski <[email protected]> 2022-08-09 14:23:48 -0400;
8da6747 More preparations for bioc submission, now with R 4.2. by mnodzenski <[email protected]> 2022-07-26 18:24:17 -0400;
d0a6854 Merge branch 'master' of https://github.com/mnodzenski/epistasisGA by mnodzenski <[email protected]> 2022-07-26 15:02:10 -0400;
40b6c57 Merge branch 'master' of https://github.com/mnodzenski/epistasisGA by mnodzenski <[email protected]> 2022-07-26 14:56:15 -0400;
2c1fb3a Merge branch 'master' of https://github.com/mnodzenski/epistasisGA by mnodzenski <[email protected]> 2022-07-26 14:56:15 -0400;
7643304 Trying to get rid of system files mistakenly pushed by mnodzenski <[email protected]> 2022-07-26 14:53:41 -0400;
f61acf9 Trying to get rid of system files mistakenly pushed by mnodzenski <[email protected]> 2022-07-26 14:53:41 -0400;
c6d1c81 More cosmetic updates to package to meet BioC guidelines, mostly for line length and unit tests. by mnodzenski <[email protected]> 2022-07-26 14:31:15 -0400;
dbe05fc Cosmetic changes to pass bioc check by mnodzenski <[email protected]> 2021-11-05 16:20:08 -0400;
e18a6b1 Add in checks for miscoded/missing genotypes and clean up some documentation issues. by mnodzenski <[email protected]> 2022-07-18 14:24:21 -0400;
d4bd652 Update chrom.fitness.score function to accept maternal-fetal interaction by mnodzenski <[email protected]> 2022-07-11 08:09:26 -0400;
d485952 Allow a different shape for mom snps in maternal/fetal networks by mnodzenski <[email protected]> 2022-05-27 10:07:28 -0400;
d83de5b Switch to computing R2 even for GxGxE by mnodzenski <[email protected]> 2022-05-24 13:18:51 -0400;
e7b8022 Fix mistake - null means and sd are chromosome size specific for GxE graphs. by mnodzenski <[email protected]> 2022-05-18 11:29:18 -0400;
cc5fbdb Minor updates to object names in the GxE test and graphics. by mnodzenski <[email protected]> 2022-05-18 10:27:18 -0400;
776d1fb Update GxE test and graphics, test a different GxE fitness score. by mnodzenski <[email protected]> 2022-05-18 09:43:16 -0400;
116c695 undoing last commit that standardized the chisq stats. by mnodzenski <[email protected]> 2022-01-10 15:22:08 -0500;
670427d Standardize chisq stats for maternal fetal interactions by mnodzenski <[email protected]> 2022-01-10 10:47:18 -0500;
cfe6184 Adding in a tweak for searching for maternal-fetal interactions. by mnodzenski <[email protected]> 2022-01-04 12:21:04 -0500;
c813c78 Attempt at a more general GxE fitness score that can handle any type of environmental exposure by mnodzenski <[email protected]> 2021-12-22 13:25:58 -0500;
96dd4c4 Use the product of the standardized inputs for the GxE fitness score. by mnodzenski <[email protected]> 2021-12-10 09:21:01 -0500;
2e8775d In combine.islands, move all individual island data to one file. by mnodzenski <[email protected]> 2021-12-09 14:33:21 -0500;
fb1e29c Try mahalanobis distance for mean weight diff, var diff, and t2. by mnodzenski <[email protected]> 2021-12-07 16:39:56 -0500;
a7bdc8d Try transmission version also using mean and variance distortion of the family weights. by mnodzenski <[email protected]> 2021-11-30 08:30:56 -0500;
1875ad6 Look at variance computed separately by exposure group. by mnodzenski <[email protected]> 2021-11-22 15:11:54 -0500;
31d0455 Try to penalize really high LD SNPs to avoid essenially pulling in duplicate SNPs. by mnodzenski <[email protected]> 2021-11-17 12:26:49 -0500;
2caf1db try version that doesn't restrict to informative families and standardizes the mean difference relative to the overall mean by mnodzenski <[email protected]> 2021-11-15 13:17:57 -0500;
88bb412 use the means in selecting mutation/crossover SNPs by mnodzenski <[email protected]> 2021-11-09 16:05:12 -0500;
39d0845 Revert "Unsuccessful attempt at a t2 using just family level data." by mnodzenski <[email protected]> 2021-11-09 15:39:30 -0500;
90efadf Unsuccessful attempt at a t2 using just family level data. by mnodzenski <[email protected]> 2021-11-09 15:32:04 -0500;
422b258 try addign in mean difference by mnodzenski <[email protected]> 2021-11-09 13:59:59 -0500;
d23fc05 trying variance based version of parents GA by mnodzenski <[email protected]> 2021-11-08 15:58:23 -0500;
4ec0900 Always use pseudo-inverse to account for non-invertible matrices. by mnodzenski <[email protected]> 2021-11-01 13:17:20 -0400;
16e0b90 Second try at using just parents for GxE, now much faster by mnodzenski <[email protected]> 2021-10-29 11:34:44 -0400;
af0da92 Attempt at using only parents, fully worked out by mnodzenski <[email protected]> 2021-10-27 17:48:20 -0400;
05a51d6 Revert "preliminary attempt at using just parent data." by mnodzenski <[email protected]> 2021-10-26 13:21:59 -0400;
8df21d3 preliminary attempt at using just parent data. by mnodzenski <[email protected]> 2021-10-25 14:12:57 -0400;
0778055 Clean up documentation by mnodzenski <[email protected]> 2021-10-19 13:54:25 -0400;
273218f Trying GxE fitness score also incorporating parental data. by mnodzenski <[email protected]> 2021-10-19 13:13:03 -0400;
d510c8f Make it an option to not exponentiate the family weights. by mnodzenski <[email protected]> 2021-10-19 10:08:34 -0400;
edbf900 Switching to two-sample hotelling with unequal variance. by mnodzenski <[email protected]> 2021-09-28 13:20:35 -0400;
7ac3022 Set the missing data to -9 at the very end, don't force users to try to do it preemptively. by mnodzenski <[email protected]> 2021-09-21 10:33:31 -0400;
763cbf9 Fix bug with exposure permutation by mnodzenski <[email protected]> 2021-08-20 08:54:03 -0400;
954591c Revert "An attempt at adding in functionality to choose optimum family weights" by mnodzenski <[email protected]> 2021-08-13 10:12:21 -0400;
f9eb355 An attempt at adding in functionality to choose optimum family weights by mnodzenski <[email protected]> 2021-07-29 16:35:31 -0400;
b97d0f5 This version of the software minimized memory usage while still running in reasonable time on the cluster, but does require enough RAM for both the full case and complement genotypes. by mnodzenski <[email protected]> 2021-07-26 13:02:40 -0400;