3f2d5dd744396ed755382b1792552491 *DESCRIPTION
b12af107b70b5149e159ed33ddbf5ec1 *NAMESPACE
a86905b31cb93d4200f8d2c3dc4323d4 *NEWS
66e02a9a4086cfb6f2a6d71d2345f344 *R/ISOpure.calculate.tac.R
936ee704d7e52a6d9223111b639d7cbb *R/ISOpure.model_optimize.cg_code.rminimize.R
79e074c017f05cd36f5b1b1b55c4675b *R/ISOpure.model_optimize.vv.vv_deriv_loglikelihood.R
950161c7a8bddba0f0bd11fbad622688 *R/ISOpure.model_optimize.vv.vv_loglikelihood.R
87007aa5c749233435ce37b2b93e15e5 *R/ISOpure.step1.CPE.R
e6795f8bf0e5ba1a8bb9186730fbc7a8 *R/ISOpure.step2.PPE.R
84cdda8c903a128bc939f0c0f6d07d47 *R/ISOpure.util.logsum.R
da1750a01c19ff4109a2969066a66a3b *R/ISOpure.util.matlab_greater_than.R
38bbb0c5ceb2887cf17dbc9a1973cf84 *R/ISOpure.util.matlab_less_than.R
4bc9ca6f7416f344bb4eb886c8f2098b *R/ISOpure.util.matlab_log.R
b7096b8cea6ae5ad16bc7d140348c497 *R/ISOpure.util.repmat.R
832c301d922da2040237fda811c6a163 *R/ISOpureS1.model_core.compute_loglikelihood.R
3352b8f1a41c5ff8e8ce099f6af1c7d7 *R/ISOpureS1.model_core.new_model.R
beeb9ff68236e1a687b75b97e9c38680 *R/ISOpureS1.model_core.optmodel.R
17e61bb8d34e26751f69d133cb43132f *R/ISOpureS1.model_optimize.kappa.kappa_compute_loglikelihood.R
82b3252189f0fd3d6ea6673ddb9b8b46 *R/ISOpureS1.model_optimize.kappa.kappa_deriv_loglikelihood.R
e2903e9a483bbb6e5926a490c6742fd6 *R/ISOpureS1.model_optimize.kappa.kappa_loglikelihood.R
a15b9ea1cc2cec8558a99c2757b078ce *R/ISOpureS1.model_optimize.mm.mm_deriv_loglikelihood.R
44572357a36289da01dd734deb9010c4 *R/ISOpureS1.model_optimize.mm.mm_loglikelihood.R
9de770d5077531276d66a25c3da71579 *R/ISOpureS1.model_optimize.omega.omega_compute_loglikelihood.R
2b58787acfd3d480c39d3afe8a31b278 *R/ISOpureS1.model_optimize.omega.omega_deriv_loglikelihood.R
84b867f54f29790a70d852d959231d21 *R/ISOpureS1.model_optimize.omega.omega_loglikelihood.R
d588055237620edec2218ced75501eb5 *R/ISOpureS1.model_optimize.opt_kappa.R
dfbc92b7fa506329cf377e6e1b73dfe8 *R/ISOpureS1.model_optimize.opt_mm.R
c0dba4081b67edd708cc1a3ed359396a *R/ISOpureS1.model_optimize.opt_omega.R
e723590b5233d4888eb6e3d243077ca2 *R/ISOpureS1.model_optimize.opt_theta.R
1c290fc9aef2faffe97aea9ba1fbd4f4 *R/ISOpureS1.model_optimize.opt_vv.R
0bd8067c15c2b74cb2fa78acdfe591a1 *R/ISOpureS1.model_optimize.theta.theta_deriv_loglikelihood.R
430826eeaa96b9caaff447d05165cc72 *R/ISOpureS1.model_optimize.theta.theta_loglikelihood.R
16154e677a18a3ce458a749737e94d0f *R/ISOpureS1.model_optimize.vv.vv_compute_loglikelihood.R
d56369dae58ca44359de1c176501856a *R/ISOpureS2.model_core.compute_loglikelihood.R
b8092e41b220dc53575e6cb7fb7d1939 *R/ISOpureS2.model_core.new_model.R
060e7fc8e0719d86d7f7c91033d42366 *R/ISOpureS2.model_core.optmodel.R
17e063aa4e8402e527d70a56d45d9cca *R/ISOpureS2.model_optimize.cc.cc_deriv_loglikelihood.R
5eeb0096562d6986490d8c5429eeedfe *R/ISOpureS2.model_optimize.cc.cc_loglikelihood.R
8713612138b985f30c694ca940c19c7c *R/ISOpureS2.model_optimize.kappa.kappa_compute_loglikelihood.R
a72e5cb7de744e80767ada1e164fcc46 *R/ISOpureS2.model_optimize.kappa.kappa_deriv_loglikelihood.R
6797af12c7ee417e706f396f5b04bda9 *R/ISOpureS2.model_optimize.kappa.kappa_loglikelihood.R
a4728651a5333d7bf6b1bcec30d6db46 *R/ISOpureS2.model_optimize.opt_cc.R
7d87010d03e624003ea5bcbbc475d113 *R/ISOpureS2.model_optimize.opt_kappa.R
43b5c6a5df0aacb9872e530af705e756 *R/ISOpureS2.model_optimize.opt_theta.R
4bf8191fa23f6ebd285a1189ac229eb1 *R/ISOpureS2.model_optimize.opt_vv.R
df3af0ba9ffbda71b6daa6254665bcef *R/ISOpureS2.model_optimize.theta.theta_deriv_loglikelihood.R
97afd0ad22266968d5dd354ffdf9d820 *R/ISOpureS2.model_optimize.theta.theta_loglikelihood.R
5dd8cd6e292e7b58571d60e632f48eb6 *R/ISOpureS2.model_optimize.vv.vv_compute_loglikelihood.R
1feff912fc7d6385ebde3aef2b4d9d46 *R/RcppExports.R
16c929a08563633f868df32b38714e0a *build/vignette.rds
52b4ec1c04f27ed6bb5a8257a4ec3c2d *inst/doc/ISOpureRGuide.Rnw
634851f4f31a45ecd3eedb0dd98a1622 *inst/doc/ISOpureRGuide.pdf
55375c883c1bc55848f3a9c9ee7004e1 *inst/extdata/Beer/alphapurities_full_dataset.txt
ac62146f993d5a05e5afd0bc587f58e6 *inst/extdata/Beer/beer.ISOpureS1model.250.transcripts.30.patients.RData
aa3d9d819687f77fedf99ba47d02b9eb *inst/extdata/Beer/beer.ISOpureS2model.250.transcripts.30.patients.RData
5ddae20028034295ed2e3c2fa1bdb6d2 *inst/extdata/Beer/beer.normaldata.250.transcripts.RData
85bd7f07dddc185c1ae09105e8a4d4a2 *inst/extdata/Beer/beer.tumordata.250.transcripts.30.patients.RData
42b9e43ebfbf9ba2f6e571e2693409fd *inst/extdata/Beer/probeset_names.txt
65fc968ee815ddfe1997bf1d95cf7579 *inst/tests/test_ISOpure_step1_beer.R
4fd9cd8e3a141987d415ea53867ed81e *inst/tests/test_ISOpure_step2_beer.R
fe65a8e3e7783b4cba9fcf64a7365e1e *man/ISOpure.calculate.tac.Rd
d050b17238026ab13637ef556eab5645 *man/ISOpure.model_optimize.cg_code.rminimize.Rd
ee0c8da1a87d175aca0872e261cc0327 *man/ISOpure.model_optimize.vv.vv_deriv_loglikelihood.Rd
17653d485416a066a947fa4565fd43b0 *man/ISOpure.model_optimize.vv.vv_loglikelihood.Rd
96621e16741d1529e754a15d46fe25db *man/ISOpure.step1.CPE.Rd
26c2660c2b2011801d7b64d1e7673b43 *man/ISOpure.step2.PPE.Rd
4d21d611eedbd5af9e83d6a6d58372ad *man/ISOpure.util.logsum.Rd
771de52e1b56c7cb30312a91c1c71754 *man/ISOpure.util.matlab_greater_than.Rd
023855cad2e5f444c336455df9dc88a1 *man/ISOpure.util.matlab_less_than.Rd
50cdefb90050d24534680bc09d36680f *man/ISOpure.util.matlab_log.Rd
1cee07c99eacd82954465b0ef6f9bede *man/ISOpure.util.repmat.Rd
8f56b42d9f1333a16bf7f7a8d52c3a7f *man/ISOpureS1.model_core.compute_loglikelihood.Rd
bc80b9bc33208caa481ff38fbf5f0c06 *man/ISOpureS1.model_core.new_model.Rd
1e60534bedb55148606fe50c5f31af42 *man/ISOpureS1.model_core.optmodel.Rd
7a5aa214393e9265a330fdb6e1e28712 *man/ISOpureS1.model_optimize.kappa.kappa_compute_loglikelihood.Rd
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0ea5241cf6caff57b1360589ac41b5af *man/ISOpureS1.model_optimize.kappa.kappa_loglikelihood.Rd
20c506e90e34d09e0dca4743f168ab97 *man/ISOpureS1.model_optimize.mm.mm_deriv_loglikelihood.Rd
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6694da8e660b06fb675f83da71b329dd *man/ISOpureS1.model_optimize.omega.omega_compute_loglikelihood.Rd
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5490e7b492dd4aaa8f5f67565bb8282d *man/ISOpureS1.model_optimize.omega.omega_loglikelihood.Rd
7ac5ed704ee8842eac66a749310698db *man/ISOpureS1.model_optimize.opt_kappa.Rd
8301440e368657bb4f4ad61805d2cb07 *man/ISOpureS1.model_optimize.opt_mm.Rd
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ffa0c6e8e173a9819b07f47c3cc15a88 *man/ISOpureS1.model_optimize.vv.vv_compute_loglikelihood.Rd
8f089f6903a2bcaac748ce7fde9a7506 *man/ISOpureS2.model_core.compute_loglikelihood.Rd
054cf0d5b31d8e6be9afdd37972dbb4b *man/ISOpureS2.model_core.new_model.Rd
53e063804381d13bfc95969906d7bd4e *man/ISOpureS2.model_core.optmodel.Rd
ab4b28893c2b4808ffa62a44caa71341 *man/ISOpureS2.model_optimize.cc.cc_deriv_loglikelihood.Rd
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eb621389eb9af3fd3dc41ca7c1595f8f *man/ISOpureS2.model_optimize.opt_cc.Rd
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7df4f06b9eba84189a0054c5f4866fb4 *man/ISOpureS2.model_optimize.opt_theta.Rd
3c6cb07b153da9bb7f0f57a22074c47e *man/ISOpureS2.model_optimize.opt_vv.Rd
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44e5ab39d414948d039309c67c825ec1 *man/ISOpureS2.model_optimize.vv.vv_compute_loglikelihood.Rd
5e374655d7c9d846122cd540d29a82ac *src/Makevars
ae98a2265ecb070a40ad0a548dd2d758 *src/RcppExports.cpp
91370afbd82e4a41c283c37f7d49e13e *src/packagename_init.c
4e8421e1f5745f359bc2abaf315bf045 *src/rcppeigen_max_over_columns_or_rows.cpp
8e91e88b55377b55345476ba9ca5ce27 *tests/test.ISOpureS1.model_optimize.kappa_vv_omega_functions.R
c7abab25366225646418c36fdc64d2a8 *tests/test.ISOpureS1.model_optimize.mm_functions.R
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ea3c9227d941d5320e378e3715966a93 *tests/test.ISOpureS2.model_optimize.cc_functions.R
fc37cdd78190e8bd693ebdfd2db9daf0 *tests/test.ISOpureS2.model_optimize.kappa_vv_functions.R
bdb0a041f350b6f6865bbf13d980ae44 *tests/test.ISOpureS2.model_optimize.theta_functions.R
b7c31a1ec953af26b2d9bd57b429dc62 *vignettes/Figures/cancer-normal-comparison-heatmap.png
a9937af7bfef38e76b174f7076fa424a *vignettes/Figures/isopure.jpg
6af5cc7f4cbc933af2f19f4693239c56 *vignettes/Figures/network-model.jpg
a332ee307d6aab27d4af06a4a7bab74e *vignettes/Figures/tumor-normal-comparison-heatmap.png
52b4ec1c04f27ed6bb5a8257a4ec3c2d *vignettes/ISOpureRGuide.Rnw
