7f3a385ae1cdf32f647a25af8a49948a *DESCRIPTION
de3b86b95e5059998117c2acc86dc65d *NAMESPACE
7ae69b3e67ad9f62d2b09c4a00a995c6 *NEWS.md
95229117b21e6c439a181a45d73318ed *R/AUC_DM_analysis.R
eb31fe6ee2df54432765f68fad07fbca *R/AllClasses.R
af9a96a903b41d5cbd10b1c3fb5ee560 *R/AllGenerics.R
6efcb68f8870e1addbe811c21643961d *R/BaumWelch.R
c5cf5cb36b79c5fcd4a502d364b957c2 *R/Viterbi.R
8382cdf46946a76a82541a148bc15d2c *R/annotation_data.R
8c96c160c12e291d6de5315c5144a689 *R/backward.R
e09b443d5f6d94f2a86451f6f568a3f9 *R/forward.R
332073df59500df764ffca2897ad0341 *R/general-functions.R
aaa2ed3fd4252035b960e01e392f9d22 *R/individual_functions.R
491681838aee3dae88043d62703c14ac *R/initialise_parameters.R
35dca77e4079da368f38ae9e2d2733e0 *R/methods.R
4813719c3f77f27ec2bd1d83b0103838 *R/pca_methylation_data.R
b0078d7e1e04904b8f816e23e1452b5e *R/plot-functions.R
aa181558acda16e8d633b93d7dba8a6f *R/plotDMR-functions.R
e60fbe2d24d39d7ed82933ad2b9942b6 *R/plot_thresholds.R
6d1d7b95851d3c300c69ebc9d2810d8c *R/sample_annotation_file.R
0335ff57216cb93f8941506d8642a618 *R/sample_methylation_file.R
dbb78f5d2842a8f94a9c4f03321e5f5a *R/summary-functions.R
d47739e500c75e88aec159c1ee25416a *R/threshold_identification.R
36f98d0e7e37ef18d989f150bd977b84 *README.md
b088751eb5145f7d45907ffb0ed331ae *build/vignette.rds
3d39550e5f98324f0b42bea4b879d4db *data/annotation_data.rda
9dbcdf878694bc66cd7216c63476575d *data/datalist
2e16af512758e9365aa855659526bdd7 *data/pca_methylation_data.rda
433e63648d43874466a377c25c832e23 *data/sample_annotation_file.rda
2b8da365050202b04ccddf822b2c5199 *data/sample_methylation_file.rda
01304fc951e9c89f571e22e68e9c5418 *inst/doc/betaHMM.R
3b47c07997215cc1d04c77c839a8b810 *inst/doc/betaHMM.Rmd
47f0ab00b883d15520d8a3a7689bba5a *inst/doc/betaHMM.html
d9fdfbda9470a85f2f8d5827b3970dba *inst/examples/betaHMM_package.R
37811a58ceabe731f4973697277123c9 *inst/logos/betaHMM_hex.png
ce4ae54bd004816441cc6e129ddbf181 *man/AUC_DM_analysis.Rd
b50f49aab74a30e88513e6978b7b9f23 *man/BaumWelch.Rd
cf656386006e5cea4b2a6e45358862ac *man/Viterbi.Rd
e18971be924432e0f6f73821ee4ed5c8 *man/annotation_data.Rd
bc67df6bbbb3751e0a80bc61bf42d93a *man/backward.Rd
5933f7d485552edf8ebe085a6060fba4 *man/betaHMM.Rd
dc2a9ca50d383a66cf8796d1e91a3000 *man/betaHMMResults.Rd
1cf3d6d368b28220ca8d9ad52452e18f *man/betaHMMrun.Rd
c860b87b67a55b0868798e69d5d2717f *man/dmcResults.Rd
de879b27016bcb825eb1827132602ff0 *man/dmc_identification.Rd
3bf1ec7178eba9d101f61ef56af3ddb3 *man/dmc_identification_run.Rd
f6a89441cce5a3a70f95ac9ee084143d *man/dmrResults.Rd
a613d3a3a56ef6d01f839e75cd68e012 *man/dmr_identification.Rd
8a973e1f058a371dd87699c4081e1ca0 *man/dmr_identification_run.Rd
d4ca294223ac8f914c34254db8e94883 *man/forward.Rd
454b24d70a64795f8239adedf641a589 *man/initialise_parameters.Rd
c521f397d174b5a9abb56aa5dac0de3c *man/packageHelpers.Rd
dcbe0e658383301c3aa708509d628613 *man/pca_methylation_data.Rd
2f548ae8ba6abecab3672716fb5b151e *man/plot.Rd
dc8c62491bf90de37632a6becc388a71 *man/sample_annotation_file.Rd
b8a132ecc363248784f0f30b7fc89f86 *man/sample_methylation_file.Rd
ea932c12bc963f90664a108e17cf387b *man/summary.Rd
a975bc76a14ca967096b772900279cdf *man/threshold_Results.Rd
cefb899b2db46b299fe1932a23b1de7e *man/threshold_identification.Rd
74f7c9a3866a7752100744b7ab7c6286 *man/threshold_identification_run.Rd
b5b6b9c61fa668a08908153f73091bed *tests/testthat.R
5d585d2432caafceccb52162816f76f3 *tests/testthat/test-betaHMM.R
3b47c07997215cc1d04c77c839a8b810 *vignettes/betaHMM.Rmd
37811a58ceabe731f4973697277123c9 *vignettes/betaHMM_hex.png
