85d4ec47a7e402fb08db467db1f5729b *DESCRIPTION
86d3f3a95c324c9479bd8986968f4327 *LICENSE
b7f36c1d79799a6006ef1d7df2b7eda9 *NAMESPACE
a8c7afb9ea9e7c183eb1dd2e75c70632 *NEWS.md
2dd5eb35640350050ebc3521b659bdbc *R/dnaEPICO-package.R
84383671872501eebac8dd7fd7a5a3d9 *R/dnamReport.R
b252d0ff5e0a112263a56fb910406d9a *R/estimateLC.R
5f047c3836027b85e8593feb0b330055 *R/estimateLCMinfiEwasWater.R
6717195ef0a71c759c1d345c64a5e51f *R/example_helpers.R
8f5d5b2dc5cf1e82d1e5ec26bf042749 *R/extractMake.R
4cfe5409447344dc806bca1f5b8ac9c4 *R/globals.R
09f133537dafcab472b8fcf7f472f07d *R/methylationGLM.R
4e9447585b04786ab0a199a85e1917ff *R/methylationGLM_steps.R
1decf1e5b0adcdeeb4133552bd40a3ff *R/methylationLME.R
f75720c3dc2a09bf018a734d26fb3c32 *R/methylationLME_steps.R
4ec0aa606888ce1b95e9bff4b0558bb4 *R/methylationValidation.R
350235126f29aae73c3988a5e44191f0 *R/preprocessingMinfiEwasWater.R
145c4634fabe36b17122c553724e1bcb *R/preprocessingMinfiEwasWater_steps.R
0dd7f32be6f6894883b47c9d6a1d1a5b *R/preprocessingMinfiEwasWater_utils.R
3f924c01956ce51924bb260c06ccb890 *R/preprocessingPheno.R
f4833e8da841ac7c7b152d7bee231ae9 *R/preprocessingPheno_steps.R
765ebc6c4be887c7e93454eb3a7d7de9 *R/readPhenotypeTargets.R
7a90c2e6e71fc7f7f20a5adb19aac09f *R/result_classes.R
52ffadf65a8d869090477bd1d20359f2 *R/svaEnmix.R
8f4dbe53757a63a54b3a1625858f0d17 *R/svaEnmix_steps.R
73ba37209dc1529a01327223f1a39875 *README.md
f06c32800676231a4db6ff2c0a6773a0 *_pkgdown.yml
faca0d3f22ecc01b2a75abfe780e5b4b *build/vignette.rds
853f4803d7795933002955ac6382c236 *inst/CITATION
f62caf32ccb41aa3f082568e9d3890b1 *inst/doc/dnaEPICO-local.R
5d4a219ba9bae4dfb99858642b73d0bd *inst/doc/dnaEPICO-local.Rmd
d8ffe59f5aa37770683640402d061071 *inst/doc/dnaEPICO-local.html
f7f7a06bbe977308b924de4ae89c3b1f *inst/doc/dnaEPICO-overview.R
4cf8880b5c08c71bb4907e7f2f7c365f *inst/doc/dnaEPICO-overview.Rmd
6ad588cbfa155332fba0ad666a7ef778 *inst/doc/dnaEPICO-overview.html
040ce16e254735fd87b38bd29a2e304a *inst/doc/dnaEPICO-pipeline.R
2aafcbc6c6803e0edfe1196d28e22773 *inst/doc/dnaEPICO-pipeline.Rmd
5588b86523eef0f8d85a1327af562c8e *inst/doc/dnaEPICO-pipeline.html
88a5c4a5a0710ed27daa9eac5ab563e8 *inst/extdata/12864_2024_10027_MOESM8_ESM.csv
efef16fab3a3f4da91830369eec85dfd *inst/extdata/cpg-viewer.js
39b600f0e212770765796bbb685f1c75 *inst/extdata/dnaEPICO.gif
259f52ebff55be59680f4557f0f5f314 *inst/extdata/dnaEPICO.svg
978b884a3bf7fa2e193a6524fbbedf7b *inst/extdata/dnaEPICORM.svg
21a428e85e57fe1fca28e614e58f983e *inst/extdata/make/Makefile.model.pipeline
3409728e2d78b5d918c1adb8d4aff32b *inst/extdata/make/Makefile.rules.pipeline
f919de2cc6413001a286970b59b86c80 *inst/extdata/saliva.txt
87a8efd35da9f7973915c711e9c54434 *inst/extdata/salivaEPIC.txt
e2e894b58f945ed1d84be2a1df851544 *inst/scripts/data.R
a14c115ac5cf966445fa65e50bd520ff *man/analyzeSvaEnmix.Rd
b1e3a1345fe84e9acceb49f3435a26f0 *man/annotateMethylationGLMSummaries.Rd
c0d330ca898c74cbdeda3f24837fea5a *man/annotateMethylationLMESummaries.Rd
7cd14b5dea0ebca4fa165c207377da56 *man/assessSamplesMinfiEwasWater.Rd
f86b3da9e94cf8ac984e36d1c7d478ea *man/buildClockFoundationInputsPreprocessingPheno.Rd
a5f0fb0cef924a7f29e79caa1b9bf1db *man/buildRawMinfiEwasWater.Rd
542d27bfcfa6f6b2288b1ad54b612976 *man/collectSignificantCpGsMethylationGLM.Rd
4a6fa659b1e93cc98764f86fde33d303 *man/collectSignificantInteractionsMethylationLME.Rd
d1c76440b2b83c96358579e83b650004 *man/combineTimepointsPreprocessingPheno.Rd
e7325c7e163c10083fa0373f7e2483a5 *man/dnaEPICO.Rd
6f02ff54862b254649c820ace2462e0e *man/dnaEPICO_dnamReport-class.Rd
718a6085e7b67c4b503f05c873353ae2 *man/dnaEPICO_dnamReport_prepared-class.Rd
d227d2fe39bcecb4e8e15d6c991e8b57 *man/dnaEPICO_dnamReport_render-class.Rd
83780e3b29b92d5c3aedec074f308760 *man/dnaEPICO_methylationGLM-class.Rd
daa876205134680c768ad68a22af9980 *man/dnaEPICO_methylationLME-class.Rd
868d3a7a2151e0698b5506bab3f52ed1 *man/dnaEPICO_preprocessingMinfiEwasWater-class.Rd
8586c98fd27d9f6949d101897de26595 *man/dnaEPICO_preprocessingPheno-class.Rd
985572a88921c81efc3fcea4c1ada1d9 *man/dnaEPICO_svaEnmix-class.Rd
6cac5fdf1fe9f6eb2e6be0c1786cd1a7 *man/dnamReport.Rd
8c633c6ec6c61e5a2e7ce3ea8bc2b031 *man/estimateLC.Rd
6f5a089ba2dd73c57732fdb92225b4f6 *man/estimateLCMinfiEwasWater.Rd
1ea606a55ba854102b9e0d308b8473cd *man/estimateSvaEnmixControls.Rd
27257909b535925fdc009980abc23be5 *man/extractMake.Rd
b1bc94e965975323b41d02b88abe27d3 *man/extractMetricsMinfiEwasWater.Rd
9b3f38a16d7a4a75b3b45dd365b62e68 *man/filterProbesMinfiEwasWater.Rd
f79eeb3073990d1f3a7235f53e2186c7 *man/filterSamplesMinfiEwasWater.Rd
b428e7e2e7396ce27fd1fef362684774 *man/fitMethylationGLMModels.Rd
0d59d8c259c2f9b3be0c5a5c4eb5ac6c *man/fitMethylationLMEModels.Rd
932b1f926b44849bba447a2f1da677be *man/loadMetricsPreprocessingPheno.Rd
f505d2d79c1596fa0d88f86d581ea14d *man/mergeSvaTargetsEnmix.Rd
7a1dd38c80cec305a640b9adca9720e4 *man/methylationGLM.Rd
19e5a9f6cd9a10dee8310a8a8454590f *man/methylationLME.Rd
4725109f0e72f9a37fe6ca2d6236ec38 *man/normalizeMinfiEwasWater.Rd
9dba8b8ab6e21eb40d8afae6a16706c0 *man/plotAssessmentMinfiEwasWater.Rd
3b215ceebeafad4361189308016e7de0 *man/plotCtrlMinfiEwasWater.Rd
017121365d1e159dc9a519865aed1a3c *man/plotMethylationGLMDiagnostics.Rd
a151a42437802da40a63c590f443e043 *man/plotMethylationGLMDistributions.Rd
103027c985550f88b323be513fea3b93 *man/plotMethylationLMEDiagnostics.Rd
07dac9c421f81f85da8dee569a5a6856 *man/plotMetricsMinfiEwasWater.Rd
ca5e23bdf1fcab35329a094b30b20862 *man/plotNormalizationMinfiEwasWater.Rd
82fa81f5b9871f98cbb98acf600f7911 *man/plotRawDensityMinfiEwasWater.Rd
8b98e0a2c6ae829358ee6d99d9fa368d *man/plotSexMinfiEwasWater.Rd
b5804aa396fe6fb003c27a9e53682074 *man/plotSvaEnmix.Rd
a89991a9d2571c8e9b82fcc821aaa7c0 *man/predictSexMinfiEwasWater.Rd
7c06ddd0131342628bc28bc4e507044e *man/prepareDnamReportInputs.Rd
371787cf094d7491813eca9c0716f1c3 *man/prepareMethylationGLMData.Rd
a54d5e922a4f1edab35c6c379cc646bd *man/prepareMethylationLMEData.Rd
770f9d2158d3a195330e0b8d0af00f16 *man/preprocessingMinfiEwasWater.Rd
282ca95bf66fd25fd187a7cac22b416a *man/preprocessingPheno.Rd
c6c34e2ecaaf74e9a35ea050d80ca957 *man/print.dnaEPICO_dnamReport.Rd
06556e61773e314494089ee2e2926e50 *man/readPhenotypeTargets.Rd
c41095bab03053c250925d21f0a8dc45 *man/readRGSetMinfiEwasWater.Rd
300766fab60af327a0d1e2ea48939c7f *man/renderDnamReport.Rd
32ec8dbb449d16ea41985f10a52c1186 *man/splitTimepointsPreprocessingPheno.Rd
3e2d2c7589af06cb608fd674181bc80c *man/summarizeMethylationGLMModels.Rd
a745f8142dd20e2b300819d4dca41eec *man/summarizeMethylationLMEModels.Rd
a621721977ac190dac31f3a17fb6fdf5 *man/summarizeTimepointsMethylationLME.Rd
22ccf1f11a13f19d9f77807e1c6a095e *man/svaEnmix.Rd
93c741663d3657bb61cdde85977c8ccf *man/writeMethylationGLMOutputs.Rd
6997db6d952fc6ab5f063ecae1d12924 *man/writeMethylationLMEOutputs.Rd
b0228252c5965c12ee26ac9fb7635371 *man/writePhenoLCMinfiEwasWater.Rd
e09f128322b4b28799b43c2a9c2b8416 *man/writePreprocessingPhenoOutputs.Rd
63a225807967dc984f9d2026d67a7e3f *man/writeSvaEnmixOutputs.Rd
0be9d73aa1722c3b9297caad23175eb3 *tests/testthat.R
bc80e16cc81c3e4f653bec0e4ab153ae *tests/testthat/test-calculation-safety.R
b29fbdc0e14e04dcee9496f3e3b1eed4 *tests/testthat/test-dnaEPICO_test.R
6184a26b3d72726926a37c88fbf3b18b *tests/testthat/test-dnamReport.R
e62c56ccbf43dc79e81018dcdac3d765 *tests/testthat/test-estimateLCMinfiEwasWater.R
8e3898db96861317fe0f570f486df392 *tests/testthat/test-extractMake.R
25fb38d2db5da25de05b5419f0e9afb1 *tests/testthat/test-methylation-values.R
49be848236da385e0ede74be89c4cead *tests/testthat/test-methylationGLM.R
08918f72becd7d7749c2c2c371da2cfb *tests/testthat/test-methylationLME.R
5c91badebc31437e88c7155fa90f7e42 *tests/testthat/test-preprocessingMinfiEwasWater.R
26cc63fa17e205e1de368d2a37ef355b *tests/testthat/test-preprocessingPheno.R
a4274aa6c90b64db4e080f3d3ef33355 *tests/testthat/test-readPhenotypeTargets.R
186f28470d06727fd56c3be81ade142a *tests/testthat/test-svaEnmix.R
5d4a219ba9bae4dfb99858642b73d0bd *vignettes/dnaEPICO-local.Rmd
4cf8880b5c08c71bb4907e7f2f7c365f *vignettes/dnaEPICO-overview.Rmd
2aafcbc6c6803e0edfe1196d28e22773 *vignettes/dnaEPICO-pipeline.Rmd
938aa917f21569abd930fc43b80c40f1 *vignettes/dnaEPICO.bib
c3d81c57aa4289449bec7b1aff031638 *vignettes/dnamReport_pipeline_overview.svg
2575b2c403cd3ed7258620e1c259829b *vignettes/methylationGLM_pipeline_overview.svg
b77f5a5fec76d0b7f5116e3bf30b19c0 *vignettes/methylationLME_pipeline_overview.svg
84a6c8073c0edfdfcc827ba8aea703df *vignettes/preprocessingMinfiEwasWater_pipeline_overview.svg
692a6d33290645f36e2bc830607c5f96 *vignettes/preprocessingPheno_pipeline_overview.svg
2ad649b4c00f49dfe71bbd7e9cf4dccb *vignettes/svaEnmix_pipeline_overview.svg
