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<h1 class="title toc-ignore">Enrichment results of depressive symptoms</h1>
<h4 class="author"><em>Xiang Zhu</em></h4>
<h4 class="date"><em>2017-04-12</em></h4>
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<p><strong>Last updated:</strong> 2018-10-05</p>
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<div id="input-data" class="section level2">
<h2>Input data</h2>
<p>Results below were generated from the GWAS summary statistics published in the paper <a href="https://www.ncbi.nlm.nih.gov/pubmed/27089181">“Genetic Variants Associated with Subjective Well-Being, Depressive Symptoms, and Neuroticism Identified Through Genome-Wide Analyses” (<em>Nature Genetics</em>, 2016)</a>. The summary data file is available at <a href="https://www.thessgac.org/data" class="uri">https://www.thessgac.org/data</a>.</p>
</div>
<div id="analysis-results" class="section level2">
<h2>Analysis results</h2>
<p>Enrichment analyses are summarized by the following three quantities.</p>
<ul>
<li><strong>BF:</strong> Bayes factor comparing the enrichment model against the baseline model;</li>
<li><strong>Outside <span class="math inline">\(\pi\)</span>:</strong> proportion of trait-associated SNPs that are “outside” the gene set;</li>
<li><strong>Inside <span class="math inline">\(\pi\)</span>:</strong> proportion of trait-associated SNPs that are “inside” the gene set.</li>
</ul>
<p>The first quantity reflects the significance of enrichment, whereas the last two capture the magnitude of enrichment. For each gene set, we report these three quantities in the last three columns of tables below, on log 10 scale.</p>
<div id="biological-pathways" class="section level3">
<h3>Biological pathways</h3>
<div id="htmlwidget-983860bb2d7d6ad3a872" style="width:100%;height:auto;" class="datatables html-widget"></div>
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PC)","Polyamine biosynthesis, arginine => agmatine => putrescine => spermidine<br/>(kegg, BioSystems)","palmitate biosynthesis<br/>(biocyc, BioSystems)","Defective ACTH causes Obesity and Pro-opiomelanocortinin deficiency (POMCD)<br/>(reactome, BioSystems)","Sterols are 12-hydroxylated by CYP8B1<br/>(reactome, PC)","Overview of telomerase RNA component gene hTerc Transcriptional Regulation<br/>(biocarta, BioCarta)","Defective CHST14 causes EDS, musculocontractural type<br/>(reactome, BioSystems)","Activation of BMF and translocation to mitochondria<br/>(reactome, PC)","icosapentaenoate biosynthesis II (metazoa)<br/>(biocyc, BioSystems)","Beta-oxidation of very long chain fatty acids<br/>(reactome, PC)","gamma-linolenate biosynthesis<br/>(biocyc, BioSystems)","γ-linolenate biosynthesis<br/>(humancyc, PC)","UTP and CTP dephosphorylation I<br/>(humancyc, PC)","miRNA Regulation of DNA Damage Response<br/>(wiki, BioSystems)","Erythrocytes take up carbon dioxide and release oxygen<br/>(reactome, PC)","L-kynurenine degradation<br/>(humancyc, PC)"],[2,4,2,2,6,2,5,8,5,3,3,2,2,3,3,3,2,3,2,2,2,3,4,9,3,6,2,3,4,2,2,4,3,2,5,3,4,6,5,4,12,2,3,4,4,2,7,4,2,2,2,3,3,3,3,2,6,4,2,7,2,3,2,2,5,2,2,5,2,3,4,2,2,2,2,2,3,3,4,2,8,2,7,2,2,4,6,2,2,6,6,3,10,5,12,13,2,9,9,13],[52,469,106,150,480,145,241,302,438,255,174,163,166,248,98,430,188,309,163,75,115,225,374,888,242,409,182,160,291,226,266,226,224,168,570,217,326,363,403,340,1006,290,271,387,273,211,464,331,194,176,171,336,269,342,214,236,230,307,143,534,134,350,198,338,354,214,197,494,152,246,376,273,96,188,199,122,264,217,378,171,725,113,441,140,128,240,306,198,192,503,509,261,961,406,1162,1250,214,785,640,1242],[395.103999382724,163.30936884441,154.424646159987,147.644092569321,147.156088494427,140.534453282216,139.760581360885,139.550038457729,105.145131027658,103.734253279802,95.6859687902645,93.9028025501519,71.516414224134,69.6814423124302,69.3073125861627,67.8513624008001,66.2358853718376,65.8678276615479,62.6721633688352,61.5871690666169,59.6651064951401,59.1906100080181,58.1535064633234,56.4952148088256,56.4727879959779,55.0313281996569,52.9026491259139,50.58883164753,50.0919366237025,45.8901489246498,45.8457839220466,45.7488113590902,45.1247838602137,42.1336108416194,41.0461597509733,40.7557679759433,40.6116597619772,40.3426317936384,39.1356948648778,38.3554526122837,36.9256292904083,35.9096507956165,35.8037622132835,35.4564365150653,35.1825714325699,33.1063685439038,33.0308149479208,32.9748980015554,32.6726633114905,32.3540388464409,31.5999141823304,31.4774287822814,31.3024320137952,31.0517154313684,30.8977038032635,30.8023151602049,30.5938616907885,30.3581088587687,28.7896513623157,28.5733380522149,26.9585087017814,26.8942773267121,26.2749963547148,26.2162903423041,25.5369080458589,25.0742276113849,24.8982131718046,23.7954008228758,23.7025451571363,23.1719655045194,22.6222536560767,22.3360566233347,20.863967561447,19.727484851428,18.6382243828811,18.2829324178349,18.1000369371622,17.3288092913893,16.9146392866367,16.8285145775658,16.7444577306692,16.2293752281701,15.7909157752421,15.7001251909109,15.0198128513365,14.240083579567,13.528145196274,13.0148487609472,12.7069105373806,12.5758902354684,12.3507259069854,11.7174254417433,11.0650540135016,11.0286300731378,10.8967972921161,10.8957435181334,10.6894629539541,6.69443628202439,-0.203267949735455,-0.252035389545167],["-5.6296<br/>[-5.9789, 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-1.4468]","-2.0334<br/>[-2.0506, -2.0137]","-2.2671<br/>[-2.2718, -2.2593]","-2.0417<br/>[-2.0438, -2.0396]","-1.3685<br/>[-1.3686, -1.3661]","-2.3050<br/>[-2.3106, -2.2959]","-1.7756<br/>[-1.7824, -1.7657]","-1.8934<br/>[-1.9029, -1.8781]","-2.1439<br/>[-2.1627, -2.1160]","-1.7281<br/>[-1.7430, -1.7131]","-2.1080<br/>[-2.1231, -2.0870]","-1.7457<br/>[-1.7513, -1.7382]","-1.7400<br/>[-1.7474, -1.7306]","-1.6158<br/>[-1.6224, -1.6070]","-2.4194<br/>[-2.4532, -2.3839]","-2.0187<br/>[-2.0353, -1.9947]","-2.2071<br/>[-2.2121, -2.1990]","-2.2491<br/>[-2.2587, -2.2340]","-2.2965<br/>[-2.3041, -2.2846]","-2.2071<br/>[-2.2300, -2.1745]","-2.6771<br/>[-2.7007, -2.6411]","-1.9344<br/>[-1.9803, -1.8899]","-2.1213<br/>[-2.1317, -2.1059]","-2.2752<br/>[-2.2865, -2.2578]","-1.7257<br/>[-1.7353, -1.7146]","-2.0135<br/>[-2.0232, -1.9984]","-2.3578<br/>[-2.3654, -2.3455]","-2.2108<br/>[-2.2187, -2.1985]","-1.6369<br/>[-1.6708, -1.6058]","-1.6354<br/>[-1.6425, -1.6263]","-1.9000<br/>[-1.9309, -1.8594]","-2.2091<br/>[-2.2251, -2.1849]","-1.7814<br/>[-1.8187, -1.7445]","-2.2172<br/>[-2.2322, -2.1959]","-2.0174<br/>[-2.0292, -1.9989]","-2.0596<br/>[-2.0715, -2.0425]","-2.0514<br/>[-2.0605, -2.0362]","-2.1728<br/>[-2.1858, -2.1525]","-1.5400<br/>[-1.5511, -1.5261]","-2.4122<br/>[-2.4264, -2.3899]","-1.5150<br/>[-1.5236, -1.5040]","-2.2302<br/>[-2.2428, -2.2107]","-1.9826<br/>[-1.9954, -1.9633]","-2.2077<br/>[-2.2274, -2.1790]","-2.2336<br/>[-2.2479, -2.2128]","-2.0239<br/>[-2.0293, -2.0149]","-1.7586<br/>[-1.8162, -1.6474]","-2.3599<br/>[-2.3920, -2.3138]","-1.8737<br/>[-1.8807, -1.8622]","-2.0819<br/>[-2.0898, -2.0690]","-2.2593<br/>[-2.2740, -2.2369]","-2.1174<br/>[-2.1348, -2.0913]","-1.3597<br/>[-1.3744, -1.3434]","-1.8186<br/>[-1.8934, -1.7603]","-1.9858<br/>[-1.9977, -1.9673]","-1.4615<br/>[-1.4806, -1.4360]","-2.0887<br/>[-2.1194, -2.0501]","-2.0277<br/>[-2.0353, -2.0147]","-2.2659<br/>[-2.2763, -2.2498]","-1.9087<br/>[-1.9311, -1.8770]","-2.5419<br/>[-2.5590, -2.5145]","-1.6962<br/>[-1.7492, -1.6298]","-2.3244<br/>[-2.3428, -2.2949]","-1.8357<br/>[-1.8448, -1.8200]","-1.6369<br/>[-1.7140, -1.5811]","-1.9330<br/>[-2.0212, -1.8634]","-2.1670<br/>[-2.1840, -2.1392]","-1.9662<br/>[-1.9948, -1.9242]","-1.9482<br/>[-1.9801, -1.9143]","-2.3877<br/>[-2.4003, -2.3674]","-2.3918<br/>[-2.4054, -2.3701]","-2.1044<br/>[-2.1154, -2.0862]","-2.6543<br/>[-2.6806, -2.6139]","-2.2916<br/>[-2.3074, -2.2675]","-2.7388<br/>[-2.7636, -2.7012]","-2.7722<br/>[-2.7956, -2.7373]","-2.0110<br/>[-2.0290, -1.9834]","-2.5818<br/>[-2.5935, -2.5624]","-4.7030<br/>[-7.5431, -4.0131]","-4.7779<br/>[-7.3574, -4.1007]"]],"container":"<table class=\"white-space: nowrap\">\n <thead>\n <tr>\n <th>Pathway name<br/>(database, repository)<\/th>\n <th># of genes<\/th>\n <th># of SNPs<\/th>\n <th>Log10 BF<\/th>\n <th>Log10 outside π<br/>(mean, 95% CI)<\/th>\n <th>Log10 inside π<br/>(mean, 95% CI)<\/th>\n <\/tr>\n <\/thead>\n<\/table>","options":{"columnDefs":[{"className":"dt-right","targets":[1,2,3]}],"order":[],"autoWidth":false,"orderClasses":false,"rowCallback":"function(row, data) {\nDTWidget.formatRound(this, row, data, 3, 3, 3, ',', '.');\n}"}},"evals":["options.rowCallback"],"jsHooks":[]}</script>
</div>
<div id="tissue-highly-expressed-genes" class="section level3">
<h3>Tissue highly expressed genes</h3>
<div id="htmlwidget-0aaad034f4771159c3b9" style="width:100%;height:auto;" class="datatables html-widget"></div>
<script type="application/json" data-for="htmlwidget-0aaad034f4771159c3b9">{"x":{"filter":"none","data":[["Spleen","Small Intestine - Terminal Ileum","Cells - EBV-transformed lymphocytes","Lung","Pancreas","Colon - Transverse","Stomach","Adrenal Gland","Esophagus - Mucosa","Breast - Mammary Tissue","Brain - Cerebellar Hemisphere","Prostate","Adipose - Subcutaneous","Uterus","Vagina","Nerve - Tibial","Brain - Hypothalamus","Brain - Hippocampus","Muscle - Skeletal","Brain - Cerebellum","Pituitary","Esophagus - Gastroesophageal Junction","Whole Blood","Skin - Sun Exposed (Lower leg)","Ovary","Heart - Left Ventricle","Adipose - Visceral (Omentum)","Brain - Anterior cingulate cortex (BA24)","Colon - Sigmoid","Skin - Not Sun Exposed (Suprapubic)","Brain - Cortex","Artery - Tibial","Esophagus - Muscularis","Thyroid","Cells - Transformed fibroblasts","Brain - Nucleus accumbens (basal ganglia)","Testis","Heart - Atrial Appendage","Artery - Coronary","Brain - Frontal Cortex (BA9)","Artery - Aorta","Liver","Brain - Caudate (basal ganglia)","Brain - Putamen (basal ganglia)"],[4665,5317,5603,5614,5783,5908,5957,6416,6242,6342,6397,6359,6374,6421,6483,6436,6566,6531,6460,6553,6618,6486,6615,6522,6683,6441,6586,6703,6605,6609,6666,6721,6696,6916,6797,6862,6807,6699,6892,6930,7005,7022,7294,7369],[-0.261312461270591,-0.27617633982261,-0.277151818427069,-0.28152771886962,-0.284872380236319,-0.288199674199491,-0.288943697105158,-0.29354989055355,-0.293850848399484,-0.294916702388208,-0.29502346990928,-0.295615753198895,-0.29561852770687,-0.295816048537127,-0.29636586477407,-0.296583930457208,-0.296841319138261,-0.297901241620168,-0.297929807016762,-0.297943009092416,-0.298147385593555,-0.298292965216574,-0.298385068790765,-0.299018085656008,-0.299183260840683,-0.299540484164338,-0.299809618399626,-0.299851673606608,-0.300428604339826,-0.300559005610248,-0.301063981493031,-0.301588256082702,-0.30199176963913,-0.302566065460181,-0.302696469435642,-0.302810410057299,-0.303144502849238,-0.303822300228082,-0.304339527688359,-0.305055180907321,-0.306534748954517,-0.306585058917436,-0.309841509564191,-0.312215060128982],["-5.6280<br/>[-5.9771, -5.4202]","-5.6277<br/>[-5.9769, -5.4199]","-5.6278<br/>[-5.9768, -5.4201]","-5.6277<br/>[-5.9768, -5.4199]","-5.6276<br/>[-5.9767, -5.4198]","-5.6275<br/>[-5.9767, -5.4197]","-5.6275<br/>[-5.9766, -5.4197]","-5.6275<br/>[-5.9765, -5.4198]","-5.6274<br/>[-5.9765, -5.4196]","-5.6274<br/>[-5.9765, -5.4196]","-5.6274<br/>[-5.9765, -5.4197]","-5.6274<br/>[-5.9765, -5.4196]","-5.6274<br/>[-5.9765, -5.4196]","-5.6274<br/>[-5.9765, -5.4196]","-5.6274<br/>[-5.9765, -5.4197]","-5.6274<br/>[-5.9765, -5.4196]","-5.6274<br/>[-5.9764, -5.4197]","-5.6273<br/>[-5.9764, -5.4196]","-5.6273<br/>[-5.9764, -5.4195]","-5.6273<br/>[-5.9764, -5.4196]","-5.6274<br/>[-5.9764, -5.4196]","-5.6273<br/>[-5.9764, -5.4195]","-5.6274<br/>[-5.9764, -5.4196]","-5.6273<br/>[-5.9764, -5.4195]","-5.6273<br/>[-5.9764, -5.4196]","-5.6273<br/>[-5.9764, -5.4194]","-5.6273<br/>[-5.9764, -5.4195]","-5.6273<br/>[-5.9764, -5.4196]","-5.6273<br/>[-5.9764, -5.4195]","-5.6273<br/>[-5.9764, -5.4195]","-5.6273<br/>[-5.9764, -5.4195]","-5.6273<br/>[-5.9764, -5.4195]","-5.6272<br/>[-5.9764, -5.4195]","-5.6273<br/>[-5.9763, -5.4196]","-5.6272<br/>[-5.9763, -5.4195]","-5.6273<br/>[-5.9763, -5.4195]","-5.6272<br/>[-5.9763, -5.4195]","-5.6272<br/>[-5.9763, -5.4194]","-5.6272<br/>[-5.9763, -5.4195]","-5.6272<br/>[-5.9763, -5.4194]","-5.6272<br/>[-5.9762, -5.4194]","-5.6272<br/>[-5.9762, -5.4194]","-5.6271<br/>[-5.9761, -5.4194]","-5.6270<br/>[-5.9761, -5.4193]"],["-5.5140<br/>[-7.6787, -4.8804]","-5.6156<br/>[-7.7378, -4.9860]","-5.3690<br/>[-7.4178, -4.7553]","-5.5828<br/>[-7.6885, -4.9548]","-5.5954<br/>[-7.6956, -4.9683]","-5.6797<br/>[-7.7677, -5.0571]","-5.6662<br/>[-7.7133, -5.0421]","-5.4511<br/>[-7.5159, -4.8292]","-5.6518<br/>[-7.7253, -5.0296]","-5.6014<br/>[-7.6719, -4.9785]","-5.5518<br/>[-7.6091, -4.9304]","-5.6307<br/>[-7.7004, -5.0070]","-5.6124<br/>[-7.6809, -4.9875]","-5.5709<br/>[-7.6392, -4.9469]","-5.5399<br/>[-7.6069, -4.9154]","-5.6055<br/>[-7.6319, -4.9815]","-5.4942<br/>[-7.5080, -4.8725]","-5.5913<br/>[-7.6421, -4.9731]","-5.6761<br/>[-7.7404, -5.0554]","-5.5705<br/>[-7.5794, -4.9516]","-5.5186<br/>[-7.5683, -4.9000]","-5.6700<br/>[-7.7322, -5.0496]","-5.5309<br/>[-7.5899, -4.9108]","-5.6793<br/>[-7.7394, -5.0579]","-5.5146<br/>[-7.5679, -4.8936]","-5.8697<br/>[-7.9350, -5.2476]","-5.6571<br/>[-7.7138, -5.0344]","-5.5370<br/>[-7.5421, -4.9157]","-5.6804<br/>[-7.6973, -5.0579]","-5.6855<br/>[-7.7413, -5.0627]","-5.6552<br/>[-7.6975, -5.0339]","-5.6231<br/>[-7.6763, -5.0019]","-5.6841<br/>[-7.7360, -5.0624]","-5.4999<br/>[-7.5371, -4.8795]","-5.6139<br/>[-7.6644, -4.9939]","-5.5600<br/>[-7.5969, -4.9414]","-5.6331<br/>[-7.6819, -5.0131]","-5.8542<br/>[-7.9078, -5.2368]","-5.6210<br/>[-7.6673, -4.9998]","-5.6331<br/>[-7.6654, -5.0154]","-5.6484<br/>[-7.6886, -5.0291]","-5.6364<br/>[-7.6685, -5.0179]","-5.5764<br/>[-7.5958, -4.9597]","-5.6533<br/>[-7.6676, -5.0375]"]],"container":"<table class=\"white-space: nowrap\">\n <thead>\n <tr>\n <th>Tissue name<\/th>\n <th># of SNPs<\/th>\n <th>Log10 BF<\/th>\n <th>Log10 outside π<br/>(mean, 95% CI)<\/th>\n <th>Log10 inside π<br/>(mean, 95% CI)<\/th>\n <\/tr>\n <\/thead>\n<\/table>","options":{"columnDefs":[{"className":"dt-right","targets":[1,2]}],"order":[],"autoWidth":false,"orderClasses":false,"rowCallback":"function(row, data) {\nDTWidget.formatRound(this, row, data, 2, 3, 3, ',', '.');\n}"}},"evals":["options.rowCallback"],"jsHooks":[]}</script>
</div>
<div id="tissue-selectively-expressed-genes" class="section level3">
<h3>Tissue selectively expressed genes</h3>
<div id="htmlwidget-9dd0ac780160f191cf9f" style="width:100%;height:auto;" class="datatables html-widget"></div>
<script type="application/json" data-for="htmlwidget-9dd0ac780160f191cf9f">{"x":{"filter":"none","data":[["Pituitary","Spleen","Liver","Skin_Sun_Exposed_(Lower_leg)","Skin_Not_Sun_Exposed_(Suprapubic)","Vagina","Esophagus_Mucosa","Cells_EBV-transformed_lymphocytes","Whole_Blood","Kidney_Cortex","Colon_Transverse","Pancreas","Testis","Lung","Muscle_Skeletal","Minor_Salivary_Gland","Small_Intestine_Terminal_Ileum","Prostate","Stomach","Breast_Mammary_Tissue","Adipose_Visceral_(Omentum)","Adipose_Subcutaneous","Cells_Transformed_fibroblasts","Brain_Cerebellum","Colon_Sigmoid","Heart_Left_Ventricle","Heart_Atrial_Appendage","Brain_Hippocampus","Brain_Amygdala","Thyroid","Brain_Nucleus_accumbens_(basal_ganglia)","Ovary","Brain_Caudate_(basal_ganglia)","Brain_Putamen_(basal_ganglia)","Brain_Cortex","Uterus","Brain_Hypothalamus","Artery_Coronary","Adrenal_Gland","Nerve_Tibial","Artery_Tibial","Brain_Spinal_cord_(cervical_c-1)","Brain_Substantia_nigra","Brain_Cerebellar_Hemisphere","Brain_Anterior_cingulate_cortex_(BA24)","Brain_Frontal_Cortex_(BA9)","Esophagus_Muscularis","Esophagus_Gastroesophageal_Junction","Artery_Aorta"],[10361,7904,8932,7323,7387,7317,7436,8423,7915,9630,8352,8210,8422,9030,9430,9186,9522,9853,10052,10535,10632,10833,11217,11729,11586,11687,11778,11876,12065,12782,12200,12344,12444,12568,12759,13203,13013,13113,13121,13280,13231,13385,13454,14306,13904,14414,14840,14710,15021],[0.699026152786999,-0.29088704557465,-0.297004105871294,-0.312851602753609,-0.313827070599076,-0.313864158268405,-0.315483723777224,-0.316700075806313,-0.31794078966025,-0.318816735974098,-0.327608309854585,-0.327700882912484,-0.330130471489163,-0.337714461199159,-0.340473204335334,-0.340834875369971,-0.344392252851179,-0.347375418855097,-0.350648244787213,-0.356613896445558,-0.357954807310607,-0.36069568253424,-0.365062820791894,-0.367992222057443,-0.368403609246369,-0.370230652833556,-0.371216766758179,-0.373040842998823,-0.375102640256718,-0.375828793131468,-0.376125710606779,-0.377122450829452,-0.378323087232389,-0.37917119594477,-0.382116258647516,-0.383284630092241,-0.383370579544014,-0.385017462900749,-0.386265370194157,-0.387714387255502,-0.38813831933341,-0.388450085258062,-0.389498059338882,-0.392536685494804,-0.393452875456124,-0.398574410463878,-0.399152640840942,-0.399545451524121,-0.403804362486595],["-5.7896<br/>[-6.2001, -5.5301]","-5.6281<br/>[-5.9762, -5.4213]","-5.6285<br/>[-5.9761, -5.4218]","-5.6270<br/>[-5.9761, -5.4192]","-5.6270<br/>[-5.9761, -5.4192]","-5.6270<br/>[-5.9761, -5.4192]","-5.6269<br/>[-5.9761, -5.4191]","-5.6271<br/>[-5.9759, -5.4195]","-5.6270<br/>[-5.9759, -5.4193]","-5.6277<br/>[-5.9757, -5.4208]","-5.6267<br/>[-5.9757, -5.4189]","-5.6266<br/>[-5.9758, -5.4188]","-5.6266<br/>[-5.9757, -5.4188]","-5.6264<br/>[-5.9755, -5.4187]","-5.6264<br/>[-5.9753, -5.4187]","-5.6263<br/>[-5.9754, -5.4185]","-5.6262<br/>[-5.9753, -5.4185]","-5.6261<br/>[-5.9751, -5.4184]","-5.6260<br/>[-5.9751, -5.4183]","-5.6259<br/>[-5.9749, -5.4182]","-5.6258<br/>[-5.9748, -5.4181]","-5.6257<br/>[-5.9748, -5.4180]","-5.6256<br/>[-5.9746, -5.4179]","-5.6256<br/>[-5.9744, -5.4180]","-5.6255<br/>[-5.9745, -5.4178]","-5.6254<br/>[-5.9744, -5.4177]","-5.6254<br/>[-5.9744, -5.4177]","-5.6253<br/>[-5.9743, -5.4176]","-5.6252<br/>[-5.9743, -5.4175]","-5.6255<br/>[-5.9741, -5.4181]","-5.6252<br/>[-5.9742, -5.4175]","-5.6252<br/>[-5.9742, -5.4175]","-5.6251<br/>[-5.9741, -5.4175]","-5.6251<br/>[-5.9741, -5.4175]","-5.6250<br/>[-5.9740, -5.4173]","-5.6250<br/>[-5.9739, -5.4175]","-5.6250<br/>[-5.9739, -5.4174]","-5.6249<br/>[-5.9739, -5.4173]","-5.6248<br/>[-5.9739, -5.4172]","-5.6248<br/>[-5.9738, -5.4171]","-5.6248<br/>[-5.9738, -5.4170]","-5.6248<br/>[-5.9738, -5.4171]","-5.6247<br/>[-5.9737, -5.4170]","-5.6247<br/>[-5.9735, -5.4173]","-5.6246<br/>[-5.9736, -5.4169]","-5.6244<br/>[-5.9734, -5.4167]","-5.6244<br/>[-5.9733, -5.4170]","-5.6244<br/>[-5.9733, -5.4168]","-5.6242<br/>[-5.9731, -5.4166]"],["-3.9995<br/>[-4.0701, -3.9266]","-4.9316<br/>[-6.9091, -4.3195]","-4.9166<br/>[-6.6846, -4.3739]","-5.7513<br/>[-7.7389, -5.1321]","-5.7502<br/>[-7.7752, -5.1337]","-5.8582<br/>[-7.8841, -5.2429]","-5.8339<br/>[-7.8162, -5.2157]","-5.3042<br/>[-7.0914, -4.7390]","-5.5268<br/>[-7.5161, -4.9132]","-5.1114<br/>[-6.7823, -4.6050]","-5.7296<br/>[-7.7076, -5.1161]","-5.9110<br/>[-7.9021, -5.2983]","-5.8529<br/>[-7.8376, -5.2413]","-5.8001<br/>[-7.7566, -5.1920]","-5.6457<br/>[-7.5980, -5.0352]","-5.8919<br/>[-7.8468, -5.2847]","-5.8270<br/>[-7.7704, -5.2188]","-5.7474<br/>[-7.6816, -5.1419]","-5.8120<br/>[-7.6844, -5.2071]","-5.8233<br/>[-7.7406, -5.2191]","-5.8408<br/>[-7.7519, -5.2374]","-5.8748<br/>[-7.7785, -5.2724]","-5.8795<br/>[-7.7735, -5.2781]","-5.7134<br/>[-7.6026, -5.1138]","-5.8272<br/>[-7.6774, -5.2253]","-5.8822<br/>[-7.7632, -5.2821]","-5.8832<br/>[-7.7622, -5.2862]","-5.9433<br/>[-7.8237, -5.3457]","-5.9485<br/>[-7.8244, -5.3509]","-5.6364<br/>[-7.3779, -5.0787]","-5.9167<br/>[-7.7897, -5.3185]","-5.8807<br/>[-7.7500, -5.2870]","-5.8924<br/>[-7.7608, -5.2967]","-5.8637<br/>[-7.6898, -5.2671]","-5.9387<br/>[-7.7979, -5.3425]","-5.7425<br/>[-7.5923, -5.1497]","-5.8488<br/>[-7.7038, -5.2539]","-5.8942<br/>[-7.7463, -5.3021]","-5.9841<br/>[-7.8349, -5.3890]","-5.9745<br/>[-7.8212, -5.3802]","-6.0574<br/>[-7.9050, -5.4617]","-5.9519<br/>[-7.7962, -5.3575]","-5.9827<br/>[-7.8242, -5.3900]","-5.7022<br/>[-7.5292, -5.1111]","-5.9557<br/>[-7.7900, -5.3623]","-5.9867<br/>[-7.8101, -5.3956]","-5.7895<br/>[-7.5627, -5.2004]","-5.8696<br/>[-7.6911, -5.2790]","-5.9702<br/>[-7.7822, -5.3826]"]],"container":"<table class=\"white-space: nowrap\">\n <thead>\n <tr>\n <th>Tissue name<\/th>\n <th># of SNPs<\/th>\n <th>Log10 BF<\/th>\n <th>Log10 outside π<br/>(mean, 95% CI)<\/th>\n <th>Log10 inside π<br/>(mean, 95% CI)<\/th>\n <\/tr>\n <\/thead>\n<\/table>","options":{"columnDefs":[{"className":"dt-right","targets":[1,2]}],"order":[],"autoWidth":false,"orderClasses":false,"rowCallback":"function(row, data) {\nDTWidget.formatRound(this, row, data, 2, 3, 3, ',', '.');\n}"}},"evals":["options.rowCallback"],"jsHooks":[]}</script>
</div>
<div id="cluster-distinctively-expressed-genes" class="section level3">
<h3>Cluster distinctively expressed genes</h3>
<div id="htmlwidget-798b325e8770e69abc2e" style="width:100%;height:auto;" class="datatables html-widget"></div>
<script type="application/json" data-for="htmlwidget-798b325e8770e69abc2e">{"x":{"filter":"none","data":[["19","12","18","1","13","15","20","7","17","10","6","14","2","11","9","3","8","16","4","5"],[6541,7719,7966,8494,8480,8556,8977,9060,9336,9212,9648,10060,10154,11103,10233,10846,10754,10894,12973,12195],[-0.250872830040795,-0.261902264903014,-0.273450257045087,-0.282809213548035,-0.286245076506903,-0.286588757656899,-0.290938112233648,-0.292883109796289,-0.294077867219248,-0.295857223246821,-0.299163140817415,-0.305053674623454,-0.305247986593833,-0.307885538147853,-0.30876310789527,-0.311188178146649,-0.312607524868716,-0.316491153559136,-0.318813021387052,-0.331220732798152],["-5.6274<br/>[-5.9764, -5.4197]","-5.6273<br/>[-5.9761, -5.4199]","-5.6270<br/>[-5.9759, -5.4193]","-5.6267<br/>[-5.9757, -5.4190]","-5.6265<br/>[-5.9757, -5.4188]","-5.6265<br/>[-5.9756, -5.4188]","-5.6265<br/>[-5.9755, -5.4188]","-5.6264<br/>[-5.9754, -5.4187]","-5.6264<br/>[-5.9754, -5.4188]","-5.6263<br/>[-5.9754, -5.4185]","-5.6262<br/>[-5.9752, -5.4186]","-5.6261<br/>[-5.9751, -5.4184]","-5.6261<br/>[-5.9750, -5.4184]","-5.6264<br/>[-5.9748, -5.4192]","-5.6259<br/>[-5.9750, -5.4182]","-5.6259<br/>[-5.9748, -5.4184]","-5.6259<br/>[-5.9748, -5.4182]","-5.6257<br/>[-5.9747, -5.4180]","-5.6262<br/>[-5.9743, -5.4193]","-5.6252<br/>[-5.9742, -5.4175]"],["-5.4629<br/>[-7.5058, -4.8421]","-5.2423<br/>[-7.2356, -4.6318]","-5.5094<br/>[-7.5074, -4.8966]","-5.6162<br/>[-7.5492, -5.0036]","-5.8756<br/>[-7.8556, -5.2616]","-5.8145<br/>[-7.7846, -5.2027]","-5.7140<br/>[-7.6847, -5.1046]","-5.7777<br/>[-7.7362, -5.1658]","-5.6381<br/>[-7.5754, -5.0308]","-5.8571<br/>[-7.8114, -5.2499]","-5.7036<br/>[-7.6365, -5.0966]","-5.7684<br/>[-7.6647, -5.1696]","-5.6998<br/>[-7.6270, -5.0927]","-5.4468<br/>[-7.1977, -4.9074]","-5.8771<br/>[-7.7607, -5.2748]","-5.6097<br/>[-7.5102, -5.0102]","-5.7288<br/>[-7.6347, -5.1251]","-5.8825<br/>[-7.7817, -5.2804]","-5.2882<br/>[-7.0274, -4.7097]","-5.9311<br/>[-7.8018, -5.3326]"]],"container":"<table class=\"white-space: nowrap\">\n <thead>\n <tr>\n <th>Cluster ID<\/th>\n <th># of SNPs<\/th>\n <th>Log10 BF<\/th>\n <th>Log10 outside π<br/>(mean, 95% CI)<\/th>\n <th>Log10 inside π<br/>(mean, 95% CI)<\/th>\n <\/tr>\n <\/thead>\n<\/table>","options":{"columnDefs":[{"className":"dt-right","targets":[1,2]}],"order":[],"autoWidth":false,"orderClasses":false,"rowCallback":"function(row, data) {\nDTWidget.formatRound(this, row, data, 2, 3, 3, ',', '.');\n}"}},"evals":["options.rowCallback"],"jsHooks":[]}</script>
<p>The relationship between tissues and clusters is shown in Figure 1 of <a href="http://journals.plos.org/plosgenetics/article?id=10.1371/journal.pgen.1006599">Dey et al. (2017)</a>; see below.</p>
<p><img src="http://journals.plos.org/plosgenetics/article/figure/image?size=large&id=10.1371/journal.pgen.1006599.g001" /></p>
</div>
</div>
<div id="session-information" class="section level2">
<h2>Session information</h2>
<div class="sourceCode" id="cb1"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb1-1" data-line-number="1">devtools<span class="op">::</span><span class="kw">session_info</span>()</a></code></pre></div>
<pre><code>Session info -------------------------------------------------------------</code></pre>
<pre><code> setting value
version R version 3.5.1 (2018-07-02)
system x86_64, darwin15.6.0
ui X11
language (EN)
collate en_US.UTF-8
tz America/Los_Angeles
date 2018-10-05 </code></pre>
<pre><code>Packages -----------------------------------------------------------------</code></pre>
<pre><code> package * version date source
assertthat 0.2.0 2017-04-11 CRAN (R 3.5.0)
backports 1.1.2 2017-12-13 CRAN (R 3.5.0)
base * 3.5.1 2018-07-05 local
bindr 0.1.1 2018-03-13 CRAN (R 3.5.0)
bindrcpp 0.2.2 2018-03-29 CRAN (R 3.5.0)
compiler 3.5.1 2018-07-05 local
crayon 1.3.4 2017-09-16 CRAN (R 3.5.0)
crosstalk 1.0.0 2016-12-21 CRAN (R 3.5.0)
datasets * 3.5.1 2018-07-05 local
devtools 1.13.6 2018-06-27 CRAN (R 3.5.0)
digest 0.6.17 2018-09-12 CRAN (R 3.5.0)
dplyr * 0.7.6 2018-06-29 CRAN (R 3.5.1)
DT * 0.4 2018-01-30 CRAN (R 3.5.0)
evaluate 0.11 2018-07-17 CRAN (R 3.5.0)
git2r 0.23.0 2018-07-17 CRAN (R 3.5.0)
glue 1.3.0 2018-07-17 CRAN (R 3.5.0)
graphics * 3.5.1 2018-07-05 local
grDevices * 3.5.1 2018-07-05 local
htmltools 0.3.6 2017-04-28 CRAN (R 3.5.0)
htmlwidgets 1.3 2018-09-30 CRAN (R 3.5.0)
httpuv 1.4.5 2018-07-19 CRAN (R 3.5.0)
jsonlite 1.5 2017-06-01 CRAN (R 3.5.0)
knitr 1.20 2018-02-20 CRAN (R 3.5.0)
later 0.7.5 2018-09-18 CRAN (R 3.5.0)
magrittr 1.5 2014-11-22 CRAN (R 3.5.0)
memoise 1.1.0 2017-04-21 CRAN (R 3.5.0)
methods * 3.5.1 2018-07-05 local
mime 0.5 2016-07-07 CRAN (R 3.5.0)
pillar 1.3.0 2018-07-14 CRAN (R 3.5.0)
pkgconfig 2.0.2 2018-08-16 CRAN (R 3.5.0)
plyr * 1.8.4 2016-06-08 CRAN (R 3.5.0)
promises 1.0.1 2018-04-13 CRAN (R 3.5.0)
purrr 0.2.5 2018-05-29 CRAN (R 3.5.0)
R.matlab * 3.6.2 2018-09-27 CRAN (R 3.5.0)
R.methodsS3 1.7.1 2016-02-16 CRAN (R 3.5.0)
R.oo 1.22.0 2018-04-22 CRAN (R 3.5.0)
R.utils 2.7.0 2018-08-27 CRAN (R 3.5.0)
R6 2.3.0 2018-10-04 CRAN (R 3.5.0)
Rcpp 0.12.19 2018-10-01 CRAN (R 3.5.0)
rlang 0.2.2 2018-08-16 CRAN (R 3.5.0)
rmarkdown 1.10 2018-06-11 CRAN (R 3.5.0)
rprojroot 1.3-2 2018-01-03 CRAN (R 3.5.0)
shiny 1.1.0 2018-05-17 CRAN (R 3.5.0)
stats * 3.5.1 2018-07-05 local
stringi 1.2.4 2018-07-20 CRAN (R 3.5.0)
stringr 1.3.1 2018-05-10 CRAN (R 3.5.0)
tibble 1.4.2 2018-01-22 CRAN (R 3.5.0)
tidyselect 0.2.4 2018-02-26 CRAN (R 3.5.0)
tools 3.5.1 2018-07-05 local
utils * 3.5.1 2018-07-05 local
whisker 0.3-2 2013-04-28 CRAN (R 3.5.0)
withr 2.1.2 2018-03-15 CRAN (R 3.5.0)
workflowr 1.1.1 2018-07-06 CRAN (R 3.5.0)
xtable 1.8-3 2018-08-29 CRAN (R 3.5.0)
yaml 2.2.0 2018-07-25 CRAN (R 3.5.0)</code></pre>
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