24d65807be9b5c9f04354d2cfb3c2579 *DESCRIPTION
1ebbd3e34237af26da5dc08a4e440464 *LICENSE
877ff74726f1ce7d42c30e824109e8c2 *NAMESPACE
2f82cf4d8000ba38c1509423b598dd8f *R/BgMethylevel.R
188915a92852946e3d90db4798da2bd2 *R/CallCandidates.R
45c7cf57818bf319fc82382ebb6f51e3 *R/CallDMRs.paramEsti.R
8b00fa513f1163446dbd30779997eaee *R/CallPeaks.multiRep.R
cf383722c1e216d47b3740d23e52a661 *R/CallPeaks.oneRep.R
4409c4e89951040828f82c9d6190a64f *R/CallPeaks.paramEsti.R
57e7146e12d022e64c86838e44973fd2 *R/ChisqTest.R
05b1146e82e1a04966b6c94286ca99d3 *R/CoefName.R
be1fc8708775cb842082108199499dc8 *R/CovR.parallel.R
faa0a364a3b7fee6ccc4cbf1a797d722 *R/DMRInfer.R
c0b08b4c7d03f988f33e4f433612c7b5 *R/DivideBins.R
1a32f4627bf9c6537822e6104ea9b359 *R/EstiMu.R
7af63ad5ccc72f2d680c6ace10750d5b *R/EstiPhi.IterativeUpdate.R
fcbe0375928a8c6a5f36fdf4692ca343 *R/EstiPhi.JointUpdate.R
ad93c0c6b81dcd8c2f6bc03fe4e2a16f *R/EstiPhi.R
9e0acddbe62912775693aaca4db46146 *R/EstiPhi.SingleUpdate.R
d81ee5a384aa6a220c436bbdb10f36b0 *R/EstiVarofMu.R
c00e0576947268af79c0f4fe4fdca280 *R/JProfileMLE.phitheta.R
e661d358801e707107f9abb49ac21195 *R/MLE.parallel.R
94f6b2e699c6ea431e69e188cbf8db46 *R/NewtonRaphson.R
c015809235c9c93424d91e0d95bf4510 *R/PostPhi.NBlogN.R
81af0bc63b20590525a37463569ecacb *R/Posterior.phi.R
4b35d95720262330f97a70e2b6161c8d *R/ShowOnePeak.R
7c1bc8428130eecff34c603e490cb138 *R/TRESS_DMRfit.R
2c14d51d84402f4b2c358f0d97c5bd38 *R/TRESS_DMRtest.R
b59058b8caab2211f611937427bd4601 *R/TRESS_peak.R
5461663bd9875d4d97cc17a12aeabc95 *R/Uniroot.truncNsd.R
d97f554105be946bcdbcf04d282cdb61 *R/WaldTest.R
3258a96b8c0eec6c4137db7de2a44939 *R/adjustHessian.R
7cf896351f490484a49e04bae3f859c5 *R/defineSrand.R
f4be95fbd8d90d5c452ab749df9f8f2c *R/esti.nullsd.lphi.R
d67afb0060b8796f5624fffa85389169 *R/exonBins.byTXDB.R
0c4e2d2850b7bdc14e4800e0cb500456 *R/filterRegions.R
8238ed75b1c7ead11033fc608b960209 *R/findBumps.R
66c466c35133f994ac0cea71278f15e6 *R/findRegion.R
37ca0d8f165adce2283abd0977237786 *R/getGeneID.R
843b00790d7a6009ce614b9594ab9769 *R/getInfer.R
62412888106f5a92877c8bb9d9b0584e *R/getLogFC.R
1cebd591a0d45457c4d89afce1148052 *R/getPeakCounts.R
699b50496af8b6144c7db8e649634bb1 *R/getStrand.R
d7e2b189b37a104c2017b55d7edd2562 *R/getWinCounts.R
8ab18cbe3c5fbd753e6941ae2b56420d *R/iCovR.R
d4c449ed85cdc4d65f2006c88b06e09a *R/iMLE.R
8df81d32bfcfca71209fa332ed5804cc *R/meRatio.R
490383af9e60445bf03ed492d331a014 *R/mix.2norm.onlysd.R
656999cea2b7bfb8b1c3472f1ccc0d27 *R/mySmooth.R
4f7658f6b89f06d9e4398107b0d19631 *R/mylogit.R
4ad7188a0b7074fe21a0ba9947590ac7 *R/mysolve.R
dda3918eed67e374e48d4104f5707929 *R/profileMLE.coef.R
d6ccb24b890fda37a8281e6272cf2434 *R/profileMLE.phi.R
501dcada72922f767f31fea187de1e3f *R/profileMLE.theta.R
31ce6fff2a5d6c023857328800ada614 *R/read.BAM.R
647b939bfd3e779fbb692e2eacff0707 *README.md
58e6c8a6507b864c65f73ca6321c0ae0 *data/Basal.rda
34d13ea1ee4dbc209fad38b1d079e6b7 *data/DMR_M3vsWT.rda
afa5145c0ffea40b4cc9541538c096a2 *data/DMR_SixWeekvsTwoWeek.rda
381a8630f10868a27246b3b130e50c3e *inst/CITATION
eed28173a6b5de2b593e7045e2b35157 *inst/NEWS
cc32b5f6e70e7ea5e20384a1e9a2fe6f *inst/extdata/examplebyBam.rda
55d5d0848fb74946245e01e313b56ecb *inst/extdata/examplebyBam_peaks.xls
a678033e78499aa6e47ca6ed3af0af7b *inst/script/exampleData.R
6b855602e270293356b35ea066f1c04f *man/Basal.Rd
defbe8e02b145d8f7e50b44bb8b98728 *man/CallCandidates.Rd
282c0596f1726a4d7c1f237625a9ac87 *man/CallDMRs.paramEsti.Rd
07e2b1f777b98758bb112b1de53d3c2c *man/CallPeaks.multiRep.Rd
92b9b0460e89720d1c2f8a03d91ee20c *man/CallPeaks.oneRep.Rd
6ee0eee0692040d9013d067b82b2401b *man/CallPeaks.paramEsti.Rd
736159f46ccad965976cea3ba7980a4c *man/CoefName.Rd
a4be153df34171b1e9ed1d537196ce9b *man/DMRInfer.Rd
13bb8056a4d36e198e9d1f53c24b0748 *man/DMR_M3vsWT.Rd
cfc4ade5b68572da39e03bd70882ca8e *man/DMR_SixWeekvsTwoWeek.Rd
6cd1fbffb78fde30aba9ad3be087ee48 *man/DivideBins.Rd
5c111b01db1e3109b886ee644f4bcde8 *man/ShowOnePeak.Rd
6fb17b240194d2ccc3bec9b7ca044381 *man/TRESS_DMRfit.Rd
f92c896c78f0bafec7def7947589930b *man/TRESS_DMRtest.Rd
f4aa5f73612dedf9da779e267c4afc27 *man/TRESS_peak.Rd
ce6f51822b0792babf8de992b7cedb1d *man/filterRegions.Rd
c9132f0154e2019d8b226419bcefa46b *man/findBumps.Rd
3b191e308fa66e2dfb35b05936883d88 *man/meRatio.Rd
