houseman-dmrs.txt

CpG	Intercept	PanTcell	CD8T	CD4T	NK	Bcell	Mono	Gran
cg00226923	0.908254648552594	0.0218475536904394	-0.0290746444815646	0.019520009724875	0.0349316733273465	-0.891558627613285	0.043308690164259	0.0442108030283962
cg16698623	0.910165601928021	0.0291908471088487	-0.0205090331614662	0.0068070685852062	0.0216508562925718	-0.804918829478583	0.0383423000849344	0.0301016053028316
cg14102807	0.861710374865453	0.0133515467273259	-0.024789511157264	-0.00679169717021715	0.0249064091110884	-0.802710142557113	0.054985251674549	0.0462940463367248
cg14127336	0.883485808414202	0.0483939005799524	-0.0405613173629306	0.0140909168912605	0.0514708954741297	-0.855206370039137	0.0631463970943434	0.0572638103519052
cg24641737	0.0741634195006262	-0.030853038777134	0.000300863984962999	-0.00486344785097266	-0.0115308877837343	0.808367400203855	-0.0336872495057226	-0.0363950545826554
cg20981615	0.528012233377504	-0.40285281488659	0.139389398121522	-0.0200902187680063	-0.450320678179238	0.340397795211808	0.290289848424227	0.188345917504462
cg02600394	0.676748993802917	-0.58788670535406	0.109560272437782	-0.0144754359051254	-0.625757684153874	0.263313671737727	0.246345521715798	0.212156864871862
cg15742700	0.750892456625374	0.0964004593761398	0.0345810838112854	-0.0110280721566924	-0.0084806574711472	-0.71056687859875	-0.670478058278152	0.085036038556365
cg03801286	0.404494948128378	0.505367307880305	-0.0273653942304828	-0.0206240864610779	0.477005435582928	0.510333969805857	-0.332791026095114	-0.339580031988152
cg25634666	0.422947643799856	0.462224480051877	-0.08197443192048	-0.042123962378522	0.46229780349238	0.487363725585318	-0.326553638323634	-0.337897343209014
cg22194129	0.81056330617648	0.0708889114934883	-0.0285475969858766	0.00660029480849171	0.0540247013834297	-0.710247701174984	0.0972964373612346	-0.00916145129145058
cg12089698	0.320025253619297	0.332003268243753	-0.145974170559955	-0.0413877767514531	0.225672648581899	-0.247689108287932	-0.254865290746315	-0.255294020182209
cg23759710	0.579891078111461	0.227647348708722	-0.0215392551916381	-0.0131038283838107	0.163019699028157	0.246366539012421	0.0963928084038928	-0.0759974955340419
cg11283860	0.391204087447826	0.545909084887539	0.00452779250143825	-0.0279228485098114	0.536988370427087	0.547998739741343	-0.191745453066884	-0.316204121103262
cg17356733	0.475461725750112	0.469305598999612	-0.013513968974286	-0.0317843298768872	0.446887363689683	0.463013987262552	-0.375815854420525	-0.378777482142773
cg00113020	0.843608259175099	0.00192749687763248	0.0403852952000484	-0.00560333410463917	-0.00750978705550742	-0.717228322097549	-0.0140643080179776	-0.00586856316856259
cg10161121	0.636040529458778	-0.571022366002796	-0.0105489717557526	0.0105437315050277	-0.56459327235982	0.120232926367912	0.249556191590753	0.246648342339584
cg16280667	0.810584804027961	-0.0527938159936551	0.0352708117294401	-0.150198783831058	0.0539698998415982	-0.746100199236664	0.0735756332856491	0.0788619595139752
cg24777950	0.43023991110125	0.487754169765329	0.00575993603642138	-0.0306990460180164	0.467117316620837	0.482939361372107	-0.337762464477966	-0.332714488716432
cg00546897	0.508681692562308	0.401034674163972	-0.0377680165868217	-0.014784604246198	0.369479952918398	0.349099957447749	-0.418964638537609	-0.174531642525083
cg24211388	0.431347027993679	0.491388590465535	-0.0206507217881299	-0.0224706838679094	0.478754578929701	0.321578741865806	-0.367895663258285	-0.362425662563024
cg18920397	0.533186559748193	-0.494121343773571	0.0135202216692545	0.00704729962809431	-0.445000522847707	-0.447638584596177	0.204256583246059	0.328144016736299
cg02497428	0.913011175643058	0.0349289729187551	-0.00060930639623138	-0.00701119453013509	0.0246506933959098	0.0345817361397683	-0.413493731148817	0.0388892147431822
cg18854666	0.709339512802502	0.231728181292235	-0.00219711321902889	-0.00475546547335495	0.263719634199702	0.128789157837579	-0.6207277448131	-0.11005976244105
cg07728874	0.702942351005065	-0.570128043018425	0.0454935776318878	0.0282743905520487	0.195803831414383	0.227255476933985	0.21856810393161	0.215148428389322
cg24841244	0.586376198849574	-0.537536503668651	0.0139730940844787	0.015957078238827	0.252713880851928	0.313530831905828	0.302737366555851	0.28551763269796
cg02780988	0.737902638224175	0.0648586577231768	-0.045746419331483	-0.0088020740868503	0.0840692575217717	-0.035177454078714	-0.644911579230224	0.0634280022356425
cg17496921	0.286327824277832	0.606625904276921	-0.0045291817115041	-0.00892898998720871	0.549608141245817	0.59607731514049	-0.24276464190428	-0.242919758798629
cg26661623	0.626896056127633	0.277992895186317	0.0134089293691282	-0.0125273845273704	0.289099768243534	0.268556746485566	-0.509658356188194	-0.203886244811189
cg12387247	0.605246625498746	0.225784848498558	-0.00718046729482253	0.0333989957445227	-0.0605551410986175	-0.577906228532149	-0.536800633710924	0.0882051786200938
cg03330678	0.369427987480852	0.547550682094592	-0.0139749763790039	-0.0334537989731728	0.551902033854722	0.500400199297696	-0.294827424393374	-0.298178178181415
cg00619207	0.438441522224125	-0.314009525563578	0.0022794033053247	-0.00789841416276909	-0.313561842217052	0.432252411107767	-0.30388223821799	0.0830344527887707
cg10266490	0.168785175284523	0.481099455413194	-0.144155008558659	0.0269804966734122	0.133548741823091	-0.0339685917307982	-0.125858169581938	-0.124832337957769
cg11456838	0.689799450601593	0.0944156008652786	0.0156925071515303	0.0081890416251876	-0.0233851765571345	-0.570939790966857	-0.00202663230236125	-0.00469354329800441
cg20748065	0.296202967810412	0.643831183918252	-0.0293992915587829	-0.0210352818999266	0.603750264596146	0.597833107762115	-0.272184731762554	-0.267817246333137
cg16098726	0.782593588900933	0.132850361104948	0.0168758000267694	0.0148467124619771	0.123208501926572	-0.647868258961606	0.0333924910357456	-0.025082126397408
cg10853416	0.718446222216315	0.124443361115079	-0.00479633330504449	0.00621856668758935	-0.0380926131513308	-0.642144822267732	-0.637162534247171	0.0269535152834545
cg18589858	0.747643135616529	0.12941251116117	-0.0123513449656557	-0.00030495029639294	0.125283028324785	0.122536737210528	-0.436525218718795	-0.00118135926734571
cg20720686	0.390170058855515	0.462796950131193	-0.00294021793731044	-0.0374399891146	0.45395683116046	0.478007350680354	0.156194556310557	-0.263043827494427
cg23140706	0.477321653290353	0.290448719515292	-0.0930981784537922	-0.0393072343507439	0.334496412655396	0.323644569777062	-0.13769276906543	-0.177248620407262
cg00515905	0.901537466671117	0.0230330499761922	-0.0298343166596783	-0.00720862914352697	-0.547297257565985	0.0414315666317184	0.0383198133122007	0.0288112958034442
cg27485921	0.348606503134606	0.393834603763446	-0.0408837904753759	-0.00869686357004385	0.444937844689832	0.507374157031422	-0.256547250738499	-0.285390017454968
cg15743985	0.27617986391246	0.33740177639404	0.0148047385523895	0.0172119225394581	0.045724174646134	-0.232780968748245	-0.218923887880196	-0.206301385050064
cg10287137	0.511421310922594	0.416676823431128	-0.029959948342391	-0.0471207519016283	0.314397532838348	0.345893659143512	-0.274292087167762	-0.341092533744165
cg04576021	0.690959794410366	0.123315588226324	0.00975639279438657	-0.0117428679686393	0.0657825359198897	-0.605417954955282	-0.00350260881759271	-0.00714893489043701
cg16522484	0.752567951852052	0.103133281478375	-0.000987133328005407	-0.0197170333367776	-0.25892228816898	0.133825798101988	0.102021828080291	-0.0178475143678997
cg27606341	0.410275395110627	0.51545940748857	0.012711245391384	-0.0155725908871778	0.490650709584115	0.33581248665664	-0.338423907406743	-0.332843493809676
cg17399166	0.843921918557361	0.0117852951048311	0.00731112156789752	-0.0127096868697986	0.0656019081546804	-0.667311119887888	-0.108197020424036	0.0467093640951206
cg13578652	0.449974074951973	-0.370693951773015	0.00317689433125393	-0.00461980699488499	-0.318641165226496	0.384988071554716	0.262812024193795	0.160293023938866
cg07730301	0.361213970330416	0.389311964211802	-0.0104942627320866	-0.0125849534950303	0.216117223193165	0.167654610222551	-0.290657348027026	-0.301064570576605
cg25226014	0.482930937039465	-0.398242212044619	0.0356016299874081	-0.0128965974975271	-0.19110903703402	0.273261046287768	0.294934842954104	0.293053512956156
cg25732252	0.43532507639343	0.187908142864984	-0.0064628992128244	0.0635198672703793	0.255011469381547	-0.379059921814605	-0.188600889343998	-0.0693481551775737
cg00974864	0.379791590319774	0.491565032393916	0.00840637599969188	-0.0401403196557785	0.471248535545168	0.507394726420839	-0.265788179880708	-0.305698001519176
cg09303642	0.465741962925237	0.43367219084602	-0.0351744911893478	-0.0159070133668284	0.36194767999045	0.248511049971838	-0.384186271275055	-0.380246237063761
cg08458487	0.361377363459457	0.555257408726863	0.00278013435235052	-0.0264215119602042	0.524695615279663	0.545207709880038	-0.300976800687022	-0.300288778888871
cg11024597	0.401401937030883	0.503366762989944	-0.0088082500050168	-0.0037307250233663	0.37788278116282	-0.0668836703543771	-0.327318545023483	-0.312174944517182
cg13650156	0.461638478026494	0.405982394023448	-0.00604867381519331	-0.0192867299896976	0.378150414062159	0.444339471794362	-0.367053699288862	-0.311464620488599
cg09914304	0.631366957163622	-0.490008992423581	-0.0918528604758399	0.0163151965263804	-0.563361608722521	0.23369442054907	0.2476521906437	0.22780608393151
cg15512851	0.248958290299671	0.501244176881145	0.0557996356659345	0.0405367093856064	-0.0437311256612741	-0.200967770207526	-0.207790732286369	-0.201091684795208
cg02656594	0.326066869967573	0.580528181335349	0.0204412914060928	-0.0237800945788121	0.493478907462971	-0.0704915559874525	-0.229080410777635	-0.224254273960487
cg04784315	0.370245733320094	0.480216833391524	0.00131803335957431	0.000393520772095452	0.442923675793565	0.336034116718684	-0.110897833316574	-0.226140183290189
cg12962778	0.725242829619246	0.1979364537404	0.0109866166437413	-0.0036070208756569	0.144361534123589	0.0808016037219781	-0.529794089621003	-0.0917514046029949
cg02630207	0.7239176665988	0.0639583846724143	0.0194716219181935	-0.0136419503247769	0.0970367084259707	-0.64106299846615	0.0562722225388579	0.0355666003573199
cg25587233	0.579602775508218	0.369693434844709	0.0184727214077622	-0.0289897041332189	0.360809700686202	0.344756695518854	-0.470227958894821	-0.210219703734594
cg26574610	0.808759555851636	0.0525572767595018	-0.0209656861385151	0.00655246635001336	0.0339845687281849	-0.711372253823677	0.0542426592567849	0.0274282658019196
cg27394566	0.71695824772892	0.158909471640113	0.00114222579184359	0.0118263065037404	0.130776448952969	-0.506491427309874	-0.13139241473225	0.0206721556848754
cg02537023	0.518492485166251	0.276908664893158	0.0355876500279581	0.00858964994506906	0.0688932057446551	-0.475029835141682	-0.249689145184408	-0.127889810134701
cg27461196	0.603855462922897	0.305989746769488	-0.043238032669368	-0.00930614937455988	0.32808367697584	0.331988230894823	-0.493663554476954	-0.49336003575384
cg00071250	0.553744319875665	-0.508899864832618	-0.0455866157705345	0.0116835399862125	-0.484592466554267	0.163010842191363	0.299634948178802	0.307277757463845
cg21969640	0.257953662799804	0.556308054280974	0.00539593362428322	0.0322501578590502	0.375814664979383	0.461463070877723	-0.233980080695816	-0.229728671411238
cg07239938	0.36141434981896	0.370683991709254	-0.112594283958443	-0.0289110663695258	0.339813503384532	0.3715247642096	-0.253511953740499	-0.270699536534125
cg22242539	0.444497556896204	0.411216383699765	-0.0969266812353211	-0.00259488186404256	0.408659598441439	0.485792428169182	-0.359879377706669	-0.353465223503529
cg12971694	0.255193415408419	0.539267290744653	0.00366664073518401	0.0711830714853888	-0.0488360181633888	-0.214110902682479	-0.208903125714555	-0.213317439944207
cg20070090	0.35884307403947	0.373708676081757	-0.0341488500165453	-0.0118198876287317	0.23496177144058	0.400926309343262	-0.246722193992195	-0.246551425202692
cg02240622	0.334577794256143	0.436378134108599	0.019058219544029	-0.0320994845085302	0.330912535953197	0.450026287983391	-0.230169334979037	-0.253178062797002
cg22456522	0.809557611095895	0.0328963723057373	-0.0110226833077567	-0.0262328709521007	0.058053825650003	0.0496035388012016	-0.680117807234322	0.0113847389489998
cg15121304	0.793877274842435	0.00187043498882862	0.0174407236968329	0.00621836068729265	-0.146896584705467	-0.56338915090496	0.0632163959974308	0.0853825293779141
cg16097772	0.367764007359695	0.50939764273252	-0.0373191499946175	0.00136007492041616	0.296432074645352	0.396790759401395	-0.29509554128201	-0.277898924815189
cg15937958	0.75103227775806	0.192241505587275	-0.0490795332402463	-0.0159776958352656	0.184668240494967	0.194955905565051	0.147034342223722	-0.142818240251055
cg15880738	0.631897123614415	-0.544872025995712	0.0129678995587374	0.0160110273107479	0.208589028716522	0.266802026802649	0.252243764604479	0.248346349140255
cg18881723	0.121081558885354	-0.0103383622066741	0.0774602533379787	-0.0471550441796978	0.553932841113719	-0.0581621038773347	-0.0599076688774043	-0.0616099713739385
cg14654385	0.412894950258164	0.501372404521947	-0.0114960388835125	-0.00931984408968569	0.377149169046699	-0.00528256395483519	-0.280119851955034	-0.327794661763838
cg12491659	0.22448399414409	0.42320966030624	-0.0636512976580896	-0.0260504670001004	0.292011549432234	-0.123086939617239	-0.116132411832986	-0.107771036711726
cg18557145	0.875964795366986	0.0521532194570138	0.00483854099082043	0.00835677349399138	0.0132787196830476	-0.539264723145572	0.0352970010053446	-0.0108941819860747
cg13253729	0.831210859238073	0.0921196407900544	-0.00846989996100772	-0.00745268752483089	0.0675699773149809	0.0152216407618888	-0.502284979260886	-0.0241724217308772
cg08044694	0.394096683715703	0.528446147924625	0.0266228925481004	-0.0110424878050752	0.461524793992807	0.48517522037116	-0.350989052545195	-0.338920702036241
cg09868035	0.414687128668445	0.335837126307085	0.0216233984935881	-0.0490022900876061	0.165943497123552	0.00700682827068002	-0.353430791676492	-0.339679975009352
cg01980222	0.346901459252641	0.318699140752181	-0.124184449985712	-0.0295000499999431	0.450077158972727	0.408104824096321	-0.250507915227874	-0.201245896752772
cg09830866	0.572993785433055	-0.531721441762633	-0.0146380746007731	0.0034936634676868	-0.493999951822388	-0.0871664804743203	0.263983911103808	0.243260649425019
cg18350391	0.760730218551112	-0.629975702018706	-0.025914011589967	0.00152948972803808	-0.115610963891065	0.120977598037516	0.173635761341487	0.153291968899936
cg07597976	0.715310357869821	0.0783994225455992	0.0400498525283604	-0.00475121259661006	-0.00911886899616243	-0.668521259270124	0.0442309817189822	0.0319575457093566
cg19963522	0.22401526284748	0.506565078176253	0.0796445834418125	0.0452807436914447	0.456115536798015	0.131352133227188	-0.144422866951631	-0.157717994482713
cg03574571	0.306988920326237	0.58017600203215	0.0227874451190828	0.00680774599829403	0.371040963616816	-0.255245503237645	-0.249799192903926	-0.239932693186453
cg09457245	0.513633437315034	0.230377635075482	-0.0403159501966969	-0.00443530915058492	0.231444865884613	-0.271865482765574	-0.272185922663087	-0.0688724893858612
cg24427660	0.483374355426619	0.451734912959205	0.0649669638576102	-0.0134775169889977	0.420261289660545	0.43623244996653	-0.0140512460236522	-0.329230141561355
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cg14182690	0.732686878640525	-0.327535596695933	-0.303134572390814	0.37336967732325	-0.559063608165986	-0.0156234183217797	0.167693290281741	0.151642286240598
cg03014680	0.74029784818609	0.0339251517796246	-0.00194050018101739	0.0158681500150078	-0.28236300298829	0.0594740850246995	-0.0834876681778994	-0.0292749107851767
cg17823175	0.626845551306737	0.222496604492575	-0.0123822022544568	-0.0108134718803051	0.246281314596588	0.2407624477164	-0.159456197322132	-0.345603965163672
cg16046376	0.649955864752854	0.280474780462134	0.0115862727710463	-0.0143618514131609	0.273565814520935	0.273056824984289	0.148460187059929	-0.228685609906349
cg11657615	0.178824836752789	0.204858348214872	0.00289851845168323	-0.0288120972313544	0.0234976053799485	-0.0229635005370507	-0.113347666688601	-0.113552860112128
cg18096388	0.40206550370163	-0.244965053669538	0.0616850499755408	-0.0643562650418827	0.162074559886389	0.032977762975907	0.0798123163812959	0.0708006712743035
cg00554250	0.20288631562082	0.161847341221146	-0.0125432630335829	0.0826261922089052	0.0193363414692321	-0.0392474680542698	-0.104243433664588	-0.0850280958375498
cg05155595	0.519558409400423	0.285597143652898	0.00784362091836885	-0.0185286772809909	0.241547287972903	0.23884548601604	-0.00438946801965626	-0.110415648906526
cg06415153	0.270825165608737	0.309073183738839	0.0524118106034874	-0.0989355506942915	0.23489766252826	0.124602009316616	-0.106800644363833	-0.120761616883637
cg10997248	0.656538722041609	-0.129023648973976	-0.0217920963372681	0.097703007463006	-0.0533188952142994	-0.366073311280194	0.0607909596160798	0.0488728485486227
cg04845063	0.266715944152494	0.236737943669418	0.0701474604815846	0.0635422069643684	0.0190897647156981	-0.0437847780017355	-0.0996424970217509	-0.0931383380944254
cg13634319	0.199878057096694	-0.154126194130644	-0.0207194889246147	0.0187229331752469	-0.111022185980663	-0.127009589736782	0.102804431702899	0.103566793328542
cg23213217	0.176831433327355	-0.0851634833057288	-0.000234789999994169	0.000860946223330331	0.18147944851183	0.0638500166984926	0.625594766713228	-0.0949247783200839
cg03368758	0.755416625925057	0.0434789407416142	0.0282134833335424	0.00936632083556315	-0.543725910474166	0.010012024068236	0.0252892940787107	-0.00313473842808499
cg00673191	0.488319377737755	0.332152588987925	-0.0288157665351312	-0.0404479042451839	0.282857877120202	0.333499655630568	0.214860382255785	-0.236824565207407
cg07086380	0.640720703999172	-0.442650418034009	0.043739358493496	-0.024539303224991	0.222734039164867	-0.125910378531704	0.162949696194396	0.195151874050583
cg15536230	0.533630548141039	0.259386601883448	0.0528589999816776	0.0235863624622762	0.118316151906724	0.165779401871815	-0.491423386156397	-0.216567098114452
cg18333690	0.156138407092748	0.218398429074015	-0.163814359529967	-0.00463108907050386	-0.0751528428009178	0.166769345178681	-0.122807969966717	-0.121943536725287
cg18399183	0.128759008638852	0.171620128034957	-0.0495069542670511	-0.0536117394737791	-0.0395922797605869	-0.0426869160368984	-0.0486550182100292	-0.0481974642735238
cg17469479	0.794527477592333	0.163566760289689	0.00495739325425092	-0.00666860035556911	0.146938950050484	0.161654403870664	0.118494026144874	-0.185851044080295
cg00431549	0.229225817559984	0.283773685399737	-0.099957981291244	0.0916547735622523	-0.0818602921720674	0.00462991495561578	-0.108460226043556	-0.0745475396626324
cg19947621	0.640664232270941	0.191971963231808	0.00447848163691022	-0.0226981343085874	0.239330773522974	0.227940996514768	-0.14658996277122	-0.100434912337567
cg16873863	0.638014196288315	0.144319987054645	0.00596041666412839	-0.0303718458376613	0.121470958306835	-0.33347199628263	-0.0676781562754744	-0.0535654712926012
cg27246571	0.790552184551396	0.187462046921324	-0.0114041355080478	-0.0133129967018079	0.174638298230715	0.183610602009208	-0.0747104613253025	-0.12899860881704
cg16501235	0.802881144389129	0.0315894556992237	-0.0113751504367053	0.0260103998743949	0.0375924659850131	-0.00584004433734312	-0.385289064440594	0.025415180654007
cg25028542	0.210723721926784	0.209742262423601	0.0353955641055194	-0.0127295189430558	0.221310584101194	0.134438475226369	-0.163217591913166	-0.160451847380196
cg03584220	0.657668131775996	-0.243254071801393	-0.0677510232014875	0.284310803921925	-0.434033129527569	0.158457360637173	0.160392872305502	0.10979944935704
cg01129847	0.305867508004864	0.384718796403475	0.0431667698623834	0.0816411483366224	-0.150909046777842	0.0207163854146519	-0.195393721578173	-0.203435495796362
cg25374813	0.349090581468691	0.32826561857487	-0.00337015000187598	-0.0215884000503006	0.322589082217021	0.155007218561387	-0.0551258014520557	-0.154231856427102
cg06131859	0.316338525895672	0.207018957455984	-0.0623577334087485	0.0093947167213343	0.0702410012393992	-0.182011302478321	-0.180076947883655	0.0742834616431012
cg06144905	0.211089116455535	0.117651166011932	0.0451525851836842	-0.0163674544023681	0.030693036510158	0.178924843148387	-0.0891622344507511	-0.0551860823765515

houseman.R

options(stringsAsFactors=FALSE)
library(parallel)
library(limma)
library(nlme)

#source('~/src/rstuff/rmodels.R')
source('src/wbcInference.R')


ilogit = function(M){
    res = exp(M) / (1 + exp(M))
    rownames(res) = rownames(M)
    colnames(res) = colnames(M)
    res
}
logit = function(b){
    res = log(b) - log(1 - b)
    rownames(res) = rownames(b)
    colnames(res) = colnames(b)
    res
}

penFitOne = function(y, Zmat){
  adj = y
  is.obs = !is.na(y)
  Z = Zmat[is.obs,,drop=FALSE]
  y = y[is.obs]
  id = rep(1,length(y))
  lmod = try(lme(y~1, random=list(id=pdIdent(~Z-1))), silent=TRUE)
  if(!inherits(lmod,"try-error")){
    adj[is.obs] = resid(lmod) + lmod$coef$fixed[1]
  }# else {
  #    message(lmod)
  #}
  list(modelFit=lmod, adjusted=adj)
}

penFitAll = function(Ymat, Zmat){
  nFeature = dim(Ymat)[1]

  mu = sigma = tau = rep(NA, nFeature)
  beta = matrix(NA, nFeature, dim(Zmat)[2])
  adjusted = matrix(NA, nFeature, dim(Ymat)[2])
  nbad = 0
  for(i in 1:nFeature){
    pf = penFitOne(Ymat[i,], Zmat)

    if(inherits(pf$modelFit,"try-error")){
      nbad = nbad + 1
      mu[i] = mean(Ymat[i,],na.rm=TRUE)
      sigma[i] = var(Ymat[i,],na.rm=TRUE)
      tau[i] = 0
      beta[i,] = 0
    }
    else{
      mu[i] = pf$modelFit$coef$fixed[1]
      sigma[i] = pf$modelFit$sigma^2
      tau[i] = getVarCov(pf$modelFit)[1,1]
      beta[i,] = pf$modelFit$coef$random$id
    }
    adjusted[i,] = pf$adjusted
  }
  message(paste("total with error in model fit:", nbad))
  list(mu=mu, beta=beta, tau=tau, sigma=sigma, adjusted=adjusted)
}

adjust.beta = function(B, top_n=500, mc.cores=24, cell.coefs="houseman-dmrs.txt", est.only=FALSE){
    if (! all(B > 0, na.rm=TRUE)){
        message("performing inverse logit to get values from 0 to 1")
        B = ilogit(B)
        print(dim(B))
        do.logit = TRUE
    } else { do.logit = FALSE }
    stopifnot(all((B > 0) & (B < 1), na.rm=TRUE))

    # after adjusting, set values < 0 or > 1 to the smallest observed value
    epsilon.min = min(B)
    epsilon.max = min(1 - B)
    
    dmr.coefs = read.delim(cell.coefs, row.names=1)
    # take shared probes. may be differences if beta is from 450k
    dmr.coefs = dmr.coefs[rownames(dmr.coefs) %in% rownames(B),]
    dmr.coefs = as.matrix(dmr.coefs[1:min(top_n, nrow(dmr.coefs)),])
    stopifnot(nrow(dmr.coefs) > 0)

    # reporter matrix
    Lwbc = diag(8)[-(1:2),]
    Lwbc[1:2,2] = 1 ; Lwbc[,1] = 1
    rownames(Lwbc) = colnames(dmr.coefs)[-(1:2)]
    colnames(Lwbc) = colnames(dmr.coefs)
    dmrs = rownames(dmr.coefs)

    message(paste0("using ", length(dmrs), " dmrs"))

    omega.mix = projectWBC(B[dmrs,],
        dmr.coefs[dmrs,],
        contrastWBC=Lwbc,
        nonnegative=TRUE,
        lessThanOne=FALSE)


    omega.mix = (1 / apply(omega.mix, 1, sum)) * omega.mix
    if(est.only){ return(omega.mix) }
    #write.table(omega.mix, sep="\t", row.names=T, quote=F, file="tmp/omega.mix.txt")
    #message("WROTE")

    message("adjusting beta (this will take a while)...")
    tmpList = lapply(1:mc.cores, function(i){ seq(from=i, to=nrow(B), by=mc.cores) })
    tmpAdj = mclapply(tmpList, function(ix){ penFitAll(B[ix,], omega.mix) }, mc.cores=mc.cores)

    adjBeta = matrix(NA, nrow(B), ncol(B))
    for (i in 1:length(tmpList)){
        adjBeta[tmpList[[i]],] = tmpAdj[[i]]$adjusted
    }
    nCpGs = nrow(B) * ncol(B)
    message(paste("% values <= 0:", sum(adjBeta <= 0, na.rm=TRUE) / nCpGs * 100))
    message(paste("% values >= 1:", sum(adjBeta >= 1, na.rm=TRUE) / nCpGs * 100))
    message("these will be changed to 0+epsilon, 1-epsilon respectively")

    adjBeta[(adjBeta <= 0)] = epsilon.min
    adjBeta[(adjBeta >= 1)] = epsilon.max
    rownames(adjBeta) = rownames(B)
    colnames(adjBeta) = colnames(B)

    if(do.logit){ return(logit(adjBeta)) };
    return(adjBeta)
}