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a |
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b/tests/diffexp/test_meta.py |
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1 |
import unittest |
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3 |
import numpy as np |
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import pandas as pd |
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import patsy |
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from inmoose.deseq2 import DESeq, makeExampleDESeqDataSet |
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from inmoose.diffexp import DEResults, meta_de |
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from inmoose.edgepy import ( |
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DGEList, |
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exactTest, |
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12 |
glmLRT, |
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glmQLFTest, |
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) |
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from inmoose.utils import Factor |
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class Test(unittest.TestCase): |
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def test_meta_de(self): |
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20 |
# test contrasts |
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21 |
dds = makeExampleDESeqDataSet(n=200, m=12, seed=42) |
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22 |
dds.obs["condition"] = Factor(np.repeat([1, 2, 3], 4)) |
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23 |
dds.obs["group"] = Factor(np.repeat([[1, 2]], 6, axis=0).flatten()) |
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24 |
dds.counts()[:, 0] = np.repeat([100, 200, 800], 4) |
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25 |
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dds.design = "~ group + condition" |
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# DE with deseq |
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dds = DESeq(dds) |
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deseq_res = dds.results() |
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31 |
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# DE with edgepy |
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d = DGEList(counts=dds.X.T, group=dds.obs["group"]) |
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d.design = patsy.dmatrix("~ group + condition", data=dds.obs) |
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d = d.estimateGLMCommonDisp() |
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36 |
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# DE with edgepy (LRT) |
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edgepy_lrt_res = glmLRT(d.glmFit()) |
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39 |
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# DE with edgepy (QL FTest) |
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edgepy_ql_res = glmQLFTest(d.glmQLFit()) |
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42 |
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# DE with edgepy (exactTest) |
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edgepy_et_res = exactTest(d) |
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45 |
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# meta-analysis |
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des = [deseq_res, edgepy_lrt_res, edgepy_ql_res, edgepy_et_res] |
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res = meta_de(des) |
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49 |
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50 |
# combined logFC and confidence intervals are controlled against metafor |
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51 |
# adjusted p-values have no external control, and are tested for non-regression |
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ref = pd.DataFrame( |
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53 |
{ |
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54 |
"combined logFC (CI_L)": [ |
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55 |
0.6660151964096146, |
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56 |
-2.6386163106710177, |
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57 |
-2.4294256191695074, |
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58 |
-0.6488512767501585, |
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59 |
-2.91706443340857, |
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60 |
-3.521554387539502, |
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61 |
-0.013715570856962955, |
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|
62 |
-2.44433271322974, |
|
|
63 |
-3.0287062069792716, |
|
|
64 |
-1.2632361321964904, |
|
|
65 |
-0.4565657144319961, |
|
|
66 |
-1.050526185309593, |
|
|
67 |
-2.898567141180949, |
|
|
68 |
-0.5981094405745551, |
|
|
69 |
0.542876997367387, |
|
|
70 |
-2.5842836601101418, |
|
|
71 |
-1.4881728468777093, |
|
|
72 |
0.2816630199971988, |
|
|
73 |
-1.621914242625586, |
|
|
74 |
-2.175531983553664, |
|
|
75 |
-2.426621491203676, |
|
|
76 |
-2.2862239530712416, |
|
|
77 |
0.6061652115075944, |
|
|
78 |
-1.7988866511533614, |
|
|
79 |
-1.3911906679104926, |
|
|
80 |
-1.6781046771044665, |
|
|
81 |
-1.5607619003814168, |
|
|
82 |
-2.7313354443639586, |
|
|
83 |
-1.819587410152225, |
|
|
84 |
-1.8461737799605058, |
|
|
85 |
-2.396354475817337, |
|
|
86 |
-4.150733072719027, |
|
|
87 |
-0.866612921109145, |
|
|
88 |
-1.6209230508004846, |
|
|
89 |
-1.3932528679807576, |
|
|
90 |
0.06535739301240662, |
|
|
91 |
-0.8614695037171913, |
|
|
92 |
-0.8949387070851511, |
|
|
93 |
-0.1885094288572462, |
|
|
94 |
-2.32066999356063, |
|
|
95 |
-1.077924632221578, |
|
|
96 |
0.37794895248328375, |
|
|
97 |
-0.5536367454374285, |
|
|
98 |
-0.21445770439079448, |
|
|
99 |
-1.037823547101704, |
|
|
100 |
-2.0371872963903646, |
|
|
101 |
-2.4346661814814206, |
|
|
102 |
-0.4321573992340394, |
|
|
103 |
-0.2907332240528021, |
|
|
104 |
-0.8539476086445773, |
|
|
105 |
-1.234310858262552, |
|
|
106 |
-2.7156517079926124, |
|
|
107 |
-2.8582388336368183, |
|
|
108 |
-1.2745838405371699, |
|
|
109 |
-2.231898985996819, |
|
|
110 |
-1.8279970283385685, |
|
|
111 |
-4.480837497725425, |
|
|
112 |
-0.8011169122478685, |
|
|
113 |
-1.9799835053398835, |
|
|
114 |
-1.0525039883843812, |
|
|
115 |
-0.11662674646446902, |
|
|
116 |
-2.544956075527203, |
|
|
117 |
-1.064065093263388, |
|
|
118 |
-0.8655309481531789, |
|
|
119 |
-3.13762536071928, |
|
|
120 |
-0.10540785386966345, |
|
|
121 |
-2.518975904098701, |
|
|
122 |
-2.0158475722803484, |
|
|
123 |
-1.6728430608728435, |
|
|
124 |
-0.5029904144572839, |
|
|
125 |
-2.7112359453355257, |
|
|
126 |
-1.608063992292449, |
|
|
127 |
-0.12750004447413454, |
|
|
128 |
-0.8225585773011765, |
|
|
129 |
-1.772440064055683, |
|
|
130 |
-0.9260166010678244, |
|
|
131 |
-2.313239524972868, |
|
|
132 |
-2.2068757891973796, |
|
|
133 |
-1.786675849820731, |
|
|
134 |
-1.0262766837558557, |
|
|
135 |
-1.642001176385648, |
|
|
136 |
0.2736409499254513, |
|
|
137 |
-1.6755199304028023, |
|
|
138 |
-2.4188282013360873, |
|
|
139 |
-1.1577393065221067, |
|
|
140 |
-2.243289671608783, |
|
|
141 |
-1.5618172554069623, |
|
|
142 |
-2.954474402652569, |
|
|
143 |
-1.4590021786483582, |
|
|
144 |
-2.371121434638752, |
|
|
145 |
0.4108524092617336, |
|
|
146 |
0.7039471918836333, |
|
|
147 |
-1.773048451498628, |
|
|
148 |
-0.3511337912563779, |
|
|
149 |
-2.29667638756921, |
|
|
150 |
-1.4953656452894795, |
|
|
151 |
0.4109470746831836, |
|
|
152 |
-1.620862282034234, |
|
|
153 |
-4.385686353557798, |
|
|
154 |
-1.264780589472257, |
|
|
155 |
-1.0905046361675372, |
|
|
156 |
-1.0403768171893486, |
|
|
157 |
-1.9921809567227817, |
|
|
158 |
-1.0215481046788315, |
|
|
159 |
-1.6201315863839372, |
|
|
160 |
-2.3497397485281812, |
|
|
161 |
-0.9990128404438292, |
|
|
162 |
-5.336487545760831, |
|
|
163 |
-1.0623709246799449, |
|
|
164 |
-0.4845713539981751, |
|
|
165 |
-1.1092279063453114, |
|
|
166 |
-3.022406150569415, |
|
|
167 |
-0.7788181579284017, |
|
|
168 |
-1.7145383153607154, |
|
|
169 |
-1.3029315696858457, |
|
|
170 |
-3.635458688461912, |
|
|
171 |
-1.7449955806992654, |
|
|
172 |
-0.37369875378310724, |
|
|
173 |
-1.0063648668773697, |
|
|
174 |
-3.121738602010506, |
|
|
175 |
-0.9469631938814649, |
|
|
176 |
-1.106923489229556, |
|
|
177 |
-1.497550281217571, |
|
|
178 |
-2.515290508312053, |
|
|
179 |
-0.9689865181728943, |
|
|
180 |
-0.04387428241650848, |
|
|
181 |
-0.37155469916385075, |
|
|
182 |
0.2678112004933926, |
|
|
183 |
-2.385590578613881, |
|
|
184 |
-0.9158592706903643, |
|
|
185 |
-1.8301813463727143, |
|
|
186 |
0.07460142020882277, |
|
|
187 |
-1.8353686638038753, |
|
|
188 |
-3.390945408814847, |
|
|
189 |
0.02301767559765966, |
|
|
190 |
-1.9324366910144262, |
|
|
191 |
-0.678599506709188, |
|
|
192 |
-2.309748259623439, |
|
|
193 |
-1.2948255656204237, |
|
|
194 |
0.35319753181102975, |
|
|
195 |
-1.0127834932344837, |
|
|
196 |
-2.176779495718015, |
|
|
197 |
-1.5315051529282733, |
|
|
198 |
0.6836811923317061, |
|
|
199 |
-2.23977305266835, |
|
|
200 |
-1.891197146518215, |
|
|
201 |
-4.784144827741974, |
|
|
202 |
-1.8037230037715726, |
|
|
203 |
-1.9295223989664199, |
|
|
204 |
-0.7340126641402587, |
|
|
205 |
-1.8476750640373827, |
|
|
206 |
-2.3842945946277867, |
|
|
207 |
-1.2424865760658015, |
|
|
208 |
-1.245280551728335, |
|
|
209 |
-1.215932212899843, |
|
|
210 |
-1.9632263729514479, |
|
|
211 |
-1.801494956920078, |
|
|
212 |
-0.2662585394490714, |
|
|
213 |
-1.5599833295880043, |
|
|
214 |
-4.881835644107957, |
|
|
215 |
-3.7493825881515503, |
|
|
216 |
-2.67304198399075, |
|
|
217 |
-1.536839751850891, |
|
|
218 |
-2.19184090843123, |
|
|
219 |
-1.94974510590935, |
|
|
220 |
-0.12555539343831423, |
|
|
221 |
-2.7007627007566892, |
|
|
222 |
-1.4724196092118091, |
|
|
223 |
-1.1455256591450884, |
|
|
224 |
-3.115445854154167, |
|
|
225 |
-1.0084793313977904, |
|
|
226 |
-0.3940975540315449, |
|
|
227 |
0.2856517318181431, |
|
|
228 |
-1.9711379193519085, |
|
|
229 |
-3.7499696990142724, |
|
|
230 |
-2.2126112079601503, |
|
|
231 |
-0.8543495093303507, |
|
|
232 |
-1.9283857091263117, |
|
|
233 |
-2.264787656888103, |
|
|
234 |
-3.7275147424298174, |
|
|
235 |
-0.554008090864221, |
|
|
236 |
-2.474562426499207, |
|
|
237 |
-0.9685815584803881, |
|
|
238 |
-0.989172560751711, |
|
|
239 |
-0.7884366564329295, |
|
|
240 |
-1.6045380562019598, |
|
|
241 |
-0.7654273118624542, |
|
|
242 |
-4.289165687959561, |
|
|
243 |
-3.5234762679288174, |
|
|
244 |
-1.3877715238168173, |
|
|
245 |
-0.4356219067620921, |
|
|
246 |
-0.4168421506416269, |
|
|
247 |
0.1318434023527142, |
|
|
248 |
-0.020915214579250163, |
|
|
249 |
-0.9953178311101134, |
|
|
250 |
-0.09157891037095012, |
|
|
251 |
-0.43160817845695565, |
|
|
252 |
-2.8193999937632803, |
|
|
253 |
-0.9965176866672529, |
|
|
254 |
-1.3939413540076844, |
|
|
255 |
], |
|
|
256 |
"combined logFC (CI_R)": [ |
|
|
257 |
3.354872058019537, |
|
|
258 |
-0.34054646318095894, |
|
|
259 |
0.35083068561892405, |
|
|
260 |
1.2758758057915247, |
|
|
261 |
0.987419819649228, |
|
|
262 |
-0.43883016404534936, |
|
|
263 |
2.1355572315208398, |
|
|
264 |
0.5080118956718125, |
|
|
265 |
-0.534349148975036, |
|
|
266 |
3.472246864111826, |
|
|
267 |
1.536101548350488, |
|
|
268 |
0.8515220599803147, |
|
|
269 |
-0.8176581829870475, |
|
|
270 |
1.447354013999258, |
|
|
271 |
2.6303737680491617, |
|
|
272 |
-0.036105150077430315, |
|
|
273 |
0.49647965833900265, |
|
|
274 |
3.0187769587400037, |
|
|
275 |
0.38285920569357956, |
|
|
276 |
-0.02243840495832705, |
|
|
277 |
0.7756234225826169, |
|
|
278 |
-0.03228481757257251, |
|
|
279 |
2.56069239477196, |
|
|
280 |
0.42803292672457405, |
|
|
281 |
0.6664263638908428, |
|
|
282 |
1.0336396693493475, |
|
|
283 |
0.4703412064756911, |
|
|
284 |
-0.7449809664746245, |
|
|
285 |
1.2827268308386777, |
|
|
286 |
0.22347520052144698, |
|
|
287 |
-0.42579173099623957, |
|
|
288 |
-1.0378149913948602, |
|
|
289 |
1.474202085650837, |
|
|
290 |
0.9832345898694661, |
|
|
291 |
0.5979839574608838, |
|
|
292 |
1.9537523108751609, |
|
|
293 |
1.4094483690114512, |
|
|
294 |
1.3045573581800696, |
|
|
295 |
2.076718012172452, |
|
|
296 |
-0.28070340978151154, |
|
|
297 |
0.9447694039293841, |
|
|
298 |
2.3437117766301405, |
|
|
299 |
1.8183642690425976, |
|
|
300 |
1.8861062700963296, |
|
|
301 |
1.0774997747736272, |
|
|
302 |
0.014536046442994888, |
|
|
303 |
-0.3734987169876831, |
|
|
304 |
1.6657293834968137, |
|
|
305 |
1.7371529269569606, |
|
|
306 |
1.6934459447290249, |
|
|
307 |
0.7288005882108818, |
|
|
308 |
-0.4582096934338016, |
|
|
309 |
0.47222573634692555, |
|
|
310 |
0.7525448340628036, |
|
|
311 |
-0.05053394143011802, |
|
|
312 |
0.666381149024404, |
|
|
313 |
-0.3611533539173757, |
|
|
314 |
1.1327677959957496, |
|
|
315 |
1.9093349096061205, |
|
|
316 |
1.6224956915201059, |
|
|
317 |
2.8092931584641434, |
|
|
318 |
-0.4675924133882219, |
|
|
319 |
0.9556382394675933, |
|
|
320 |
1.1537936002185782, |
|
|
321 |
0.4719726272864868, |
|
|
322 |
1.8940426428930035, |
|
|
323 |
-0.370165159637702, |
|
|
324 |
0.5148047144587685, |
|
|
325 |
0.37474384949352624, |
|
|
326 |
3.582528610121325, |
|
|
327 |
1.266931510128373, |
|
|
328 |
2.2158467226115492, |
|
|
329 |
3.071101744852342, |
|
|
330 |
1.1813346784457122, |
|
|
331 |
0.18990362116929815, |
|
|
332 |
1.1106002066088052, |
|
|
333 |
-0.12768912119813525, |
|
|
334 |
-0.1844407501803229, |
|
|
335 |
0.25835875418293686, |
|
|
336 |
1.1774869629070284, |
|
|
337 |
0.3507702603130787, |
|
|
338 |
2.7960199923829494, |
|
|
339 |
0.6503959195118854, |
|
|
340 |
-0.02699953769695007, |
|
|
341 |
1.5711833206054435, |
|
|
342 |
0.4520306257582095, |
|
|
343 |
0.5672425711692818, |
|
|
344 |
0.766116704264352, |
|
|
345 |
0.5643657171094311, |
|
|
346 |
-0.27795639060702126, |
|
|
347 |
2.366747950705241, |
|
|
348 |
2.77534421368124, |
|
|
349 |
0.41134113503556835, |
|
|
350 |
1.969588958548259, |
|
|
351 |
1.2844090294384958, |
|
|
352 |
0.9380549081602017, |
|
|
353 |
3.274251586886894, |
|
|
354 |
0.6590123200119615, |
|
|
355 |
0.750549465611706, |
|
|
356 |
2.018855699691608, |
|
|
357 |
1.0562073319536494, |
|
|
358 |
0.950802281270808, |
|
|
359 |
0.5938590357378501, |
|
|
360 |
1.0494322805270517, |
|
|
361 |
1.5076695060610152, |
|
|
362 |
0.9887948817674262, |
|
|
363 |
4.264921321686238, |
|
|
364 |
1.0328063734921642, |
|
|
365 |
0.8621704647652939, |
|
|
366 |
4.993500038553787, |
|
|
367 |
0.9499110359553256, |
|
|
368 |
-0.8997966342353689, |
|
|
369 |
1.4795464281564392, |
|
|
370 |
0.874904298760736, |
|
|
371 |
0.7724717737068273, |
|
|
372 |
0.8436676453709686, |
|
|
373 |
0.38875016354958924, |
|
|
374 |
1.6996550100286307, |
|
|
375 |
1.0180844678588887, |
|
|
376 |
-0.8432083259898191, |
|
|
377 |
1.814332444242015, |
|
|
378 |
0.89595219174541, |
|
|
379 |
0.47768062281587376, |
|
|
380 |
-0.6122504151106485, |
|
|
381 |
0.9676127377450849, |
|
|
382 |
1.9942096848086273, |
|
|
383 |
2.5322997447126463, |
|
|
384 |
2.6138264680652976, |
|
|
385 |
0.06389822388153621, |
|
|
386 |
1.3473614017305102, |
|
|
387 |
0.2707537486533764, |
|
|
388 |
4.160256742758929, |
|
|
389 |
0.3225311846941912, |
|
|
390 |
-0.916644886148936, |
|
|
391 |
2.691811189135298, |
|
|
392 |
0.5218401717051796, |
|
|
393 |
1.2741589329453422, |
|
|
394 |
0.12126997384548743, |
|
|
395 |
0.5949804141792554, |
|
|
396 |
2.316820003047362, |
|
|
397 |
1.0110795928142386, |
|
|
398 |
0.6586624521693996, |
|
|
399 |
3.422985512826824, |
|
|
400 |
2.7421890347062328, |
|
|
401 |
1.5513174592326577, |
|
|
402 |
0.25964239369840003, |
|
|
403 |
0.20181520548352871, |
|
|
404 |
0.9264018383524469, |
|
|
405 |
0.015928832730718212, |
|
|
406 |
1.28513806241418, |
|
|
407 |
0.7355117760711144, |
|
|
408 |
0.8107859106491883, |
|
|
409 |
2.436102208526566, |
|
|
410 |
1.0699877757552179, |
|
|
411 |
0.8751364190659427, |
|
|
412 |
0.05081803315723321, |
|
|
413 |
0.22775593873046085, |
|
|
414 |
1.6470249080421566, |
|
|
415 |
1.8052433343747047, |
|
|
416 |
-0.6862411763247649, |
|
|
417 |
0.7657421312167374, |
|
|
418 |
-0.48935736430145216, |
|
|
419 |
0.3473665242861057, |
|
|
420 |
0.9672738541238843, |
|
|
421 |
0.37303455240566996, |
|
|
422 |
2.348076008955688, |
|
|
423 |
0.22513005048675083, |
|
|
424 |
0.6067512405141617, |
|
|
425 |
0.8955766331258332, |
|
|
426 |
-0.6949808575425094, |
|
|
427 |
1.313934433369968, |
|
|
428 |
1.6405906148006886, |
|
|
429 |
2.68193589852294, |
|
|
430 |
0.7671934502323494, |
|
|
431 |
2.818888058186232, |
|
|
432 |
-0.18521862612875628, |
|
|
433 |
1.0476709254412027, |
|
|
434 |
0.5922832182532727, |
|
|
435 |
-0.08490117418915877, |
|
|
436 |
-0.7311606079226332, |
|
|
437 |
1.3351236101816348, |
|
|
438 |
-0.4398791608381776, |
|
|
439 |
1.151171699680487, |
|
|
440 |
1.743948784448906, |
|
|
441 |
1.2591808745192232, |
|
|
442 |
0.4065967359112883, |
|
|
443 |
1.2607500621625511, |
|
|
444 |
-1.182757686341431, |
|
|
445 |
-0.9549093767155574, |
|
|
446 |
0.5752653648553867, |
|
|
447 |
1.4776432917947777, |
|
|
448 |
1.8303526779984838, |
|
|
449 |
2.45286628466279, |
|
|
450 |
1.9298533345564415, |
|
|
451 |
1.351808248409464, |
|
|
452 |
2.2091228037508985, |
|
|
453 |
1.5322246498088472, |
|
|
454 |
-0.5191787229012983, |
|
|
455 |
1.0055531958855577, |
|
|
456 |
0.8993415317328557, |
|
|
457 |
], |
|
|
458 |
"combined logFC": [ |
|
|
459 |
2.010443627214576, |
|
|
460 |
-1.4895813869259882, |
|
|
461 |
-1.0392974667752917, |
|
|
462 |
0.31351226452068304, |
|
|
463 |
-0.964822306879671, |
|
|
464 |
-1.9801922757924255, |
|
|
465 |
1.0609208303319384, |
|
|
466 |
-0.9681604087789637, |
|
|
467 |
-1.7815276779771538, |
|
|
468 |
1.1045053659576676, |
|
|
469 |
0.539767916959246, |
|
|
470 |
-0.09950206266463923, |
|
|
471 |
-1.8581126620839983, |
|
|
472 |
0.4246222867123514, |
|
|
473 |
1.5866253827082744, |
|
|
474 |
-1.3101944050937862, |
|
|
475 |
-0.4958465942693533, |
|
|
476 |
1.6502199893686014, |
|
|
477 |
-0.6195275184660032, |
|
|
478 |
-1.0989851942559956, |
|
|
479 |
-0.8254990343105295, |
|
|
480 |
-1.159254385321907, |
|
|
481 |
1.5834288031397772, |
|
|
482 |
-0.6854268622143936, |
|
|
483 |
-0.36238215200982493, |
|
|
484 |
-0.32223250387755953, |
|
|
485 |
-0.5452103469528629, |
|
|
486 |
-1.7381582054192914, |
|
|
487 |
-0.2684302896567735, |
|
|
488 |
-0.8113492897195295, |
|
|
489 |
-1.4110731034067885, |
|
|
490 |
-2.5942740320569437, |
|
|
491 |
0.303794582270846, |
|
|
492 |
-0.3188442304655092, |
|
|
493 |
-0.39763445525993685, |
|
|
494 |
1.0095548519437838, |
|
|
495 |
0.27398943264712994, |
|
|
496 |
0.2048093255474592, |
|
|
497 |
0.944104291657603, |
|
|
498 |
-1.3006867016710706, |
|
|
499 |
-0.06657761414609703, |
|
|
500 |
1.3608303645567121, |
|
|
501 |
0.6323637618025846, |
|
|
502 |
0.8358242828527676, |
|
|
503 |
0.019838113835961624, |
|
|
504 |
-1.0113256249736848, |
|
|
505 |
-1.4040824492345518, |
|
|
506 |
0.6167859921313871, |
|
|
507 |
0.7232098514520792, |
|
|
508 |
0.41974916804222373, |
|
|
509 |
-0.252755135025835, |
|
|
510 |
-1.586930700713207, |
|
|
511 |
-1.1930065486449464, |
|
|
512 |
-0.26101950323718315, |
|
|
513 |
-1.1412164637134685, |
|
|
514 |
-0.5808079396570822, |
|
|
515 |
-2.4209954258214, |
|
|
516 |
0.1658254418739405, |
|
|
517 |
-0.03532429786688163, |
|
|
518 |
0.2849958515678623, |
|
|
519 |
1.3463332059998372, |
|
|
520 |
-1.5062742444577124, |
|
|
521 |
-0.05421342689789732, |
|
|
522 |
0.14413132603269962, |
|
|
523 |
-1.3328263667163966, |
|
|
524 |
0.89431739451167, |
|
|
525 |
-1.4445705318682016, |
|
|
526 |
-0.7505214289107899, |
|
|
527 |
-0.6490496056896586, |
|
|
528 |
1.5397690978320207, |
|
|
529 |
-0.7221522176035764, |
|
|
530 |
0.30389136515955006, |
|
|
531 |
1.4718008501891038, |
|
|
532 |
0.1793880505722678, |
|
|
533 |
-0.7912682214431924, |
|
|
534 |
0.0922918027704904, |
|
|
535 |
-1.2204643230855017, |
|
|
536 |
-1.1956582696888511, |
|
|
537 |
-0.764158547818897, |
|
|
538 |
0.07560513957558634, |
|
|
539 |
-0.6456154580362846, |
|
|
540 |
1.5348304711542002, |
|
|
541 |
-0.5125620054454585, |
|
|
542 |
-1.2229138695165187, |
|
|
543 |
0.20672200704166846, |
|
|
544 |
-0.8956295229252867, |
|
|
545 |
-0.4972873421188403, |
|
|
546 |
-1.0941788491941085, |
|
|
547 |
-0.44731823076946353, |
|
|
548 |
-1.3245389126228866, |
|
|
549 |
1.3888001799834873, |
|
|
550 |
1.7396457027824366, |
|
|
551 |
-0.6808536582315298, |
|
|
552 |
0.8092275836459406, |
|
|
553 |
-0.5061336790653573, |
|
|
554 |
-0.27865536856463896, |
|
|
555 |
1.842599330785039, |
|
|
556 |
-0.4809249810111363, |
|
|
557 |
-1.817568443973046, |
|
|
558 |
0.3770375551096756, |
|
|
559 |
-0.017148652106944023, |
|
|
560 |
-0.044787267959270266, |
|
|
561 |
-0.6991609604924658, |
|
|
562 |
0.01394208792411003, |
|
|
563 |
-0.056231040161460966, |
|
|
564 |
-0.6804724333803774, |
|
|
565 |
1.6329542406212045, |
|
|
566 |
-2.1518405861343335, |
|
|
567 |
-0.10010022995732543, |
|
|
568 |
2.2544643422778057, |
|
|
569 |
-0.07965843519499288, |
|
|
570 |
-1.961101392402392, |
|
|
571 |
0.3503641351140188, |
|
|
572 |
-0.41981700829998975, |
|
|
573 |
-0.26522989798950924, |
|
|
574 |
-1.3958955215454716, |
|
|
575 |
-0.6781227085748381, |
|
|
576 |
0.6629781281227617, |
|
|
577 |
0.005859800490759473, |
|
|
578 |
-1.9824734640001627, |
|
|
579 |
0.43368462518027506, |
|
|
580 |
-0.10548564874207311, |
|
|
581 |
-0.5099348292008486, |
|
|
582 |
-1.5637704617113508, |
|
|
583 |
-0.0006868902139046985, |
|
|
584 |
0.9751677011960594, |
|
|
585 |
1.0803725227743979, |
|
|
586 |
1.440818834279345, |
|
|
587 |
-1.1608461773661722, |
|
|
588 |
0.21575106552007295, |
|
|
589 |
-0.779713798859669, |
|
|
590 |
2.117429081483876, |
|
|
591 |
-0.7564187395548421, |
|
|
592 |
-2.1537951474818917, |
|
|
593 |
1.357414432366479, |
|
|
594 |
-0.7052982596546232, |
|
|
595 |
0.29777971311807716, |
|
|
596 |
-1.094239142888976, |
|
|
597 |
-0.3499225757205842, |
|
|
598 |
1.3350087674291957, |
|
|
599 |
-0.0008519502101226178, |
|
|
600 |
-0.7590585217743078, |
|
|
601 |
0.9457401799492752, |
|
|
602 |
1.7129351135189694, |
|
|
603 |
-0.3442277967178461, |
|
|
604 |
-0.8157773764099074, |
|
|
605 |
-2.2911648111292227, |
|
|
606 |
-0.43866058270956276, |
|
|
607 |
-0.9567967831178508, |
|
|
608 |
0.2755626991369606, |
|
|
609 |
-0.5560816439831341, |
|
|
610 |
-0.7867543419892992, |
|
|
611 |
0.5968078162303823, |
|
|
612 |
-0.08764638798655852, |
|
|
613 |
-0.17039789691695012, |
|
|
614 |
-0.9562041698971073, |
|
|
615 |
-0.7868695090948086, |
|
|
616 |
0.6903831842965426, |
|
|
617 |
0.12263000239335031, |
|
|
618 |
-2.7840384102163607, |
|
|
619 |
-1.4918202284674065, |
|
|
620 |
-1.5811996741461012, |
|
|
621 |
-0.5947366137823926, |
|
|
622 |
-0.6122835271536728, |
|
|
623 |
-0.78835527675184, |
|
|
624 |
1.111260307758687, |
|
|
625 |
-1.2378163251349692, |
|
|
626 |
-0.4328341843488237, |
|
|
627 |
-0.12497451300962753, |
|
|
628 |
-1.9052133558483382, |
|
|
629 |
0.15272755098608884, |
|
|
630 |
0.6232465303845719, |
|
|
631 |
1.4837938151705414, |
|
|
632 |
-0.6019722345597796, |
|
|
633 |
-0.4655408204140199, |
|
|
634 |
-1.1989149170444533, |
|
|
635 |
0.09666070805542601, |
|
|
636 |
-0.6680512454365195, |
|
|
637 |
-1.1748444155386308, |
|
|
638 |
-2.2293376751762253, |
|
|
639 |
0.390557759658707, |
|
|
640 |
-1.4572207936686923, |
|
|
641 |
0.09129507060004953, |
|
|
642 |
0.37738811184859755, |
|
|
643 |
0.23537210904314693, |
|
|
644 |
-0.5989706601453357, |
|
|
645 |
0.2476613751500485, |
|
|
646 |
-2.735961687150496, |
|
|
647 |
-2.2391928223221873, |
|
|
648 |
-0.4062530794807153, |
|
|
649 |
0.5210106925163428, |
|
|
650 |
0.7067552636784284, |
|
|
651 |
1.292354843507752, |
|
|
652 |
0.9544690599885957, |
|
|
653 |
0.1782452086496753, |
|
|
654 |
1.0587719466899743, |
|
|
655 |
0.5503082356759458, |
|
|
656 |
-1.6692893583322892, |
|
|
657 |
0.00451775460915238, |
|
|
658 |
-0.24729991113741429, |
|
|
659 |
], |
|
|
660 |
"adjusted combined pval": [ |
|
|
661 |
0.002710867577467824, |
|
|
662 |
0.5286922590236601, |
|
|
663 |
0.3635268253933128, |
|
|
664 |
0.9999997373138294, |
|
|
665 |
0.9999997373138294, |
|
|
666 |
0.40841535987809763, |
|
|
667 |
0.8552303143709908, |
|
|
668 |
0.45397729003343607, |
|
|
669 |
0.249091508520245, |
|
|
670 |
0.2061819814543404, |
|
|
671 |
0.9999997373138294, |
|
|
672 |
0.9999997373138294, |
|
|
673 |
0.249091508520245, |
|
|
674 |
0.9999997373138294, |
|
|
675 |
0.40841535987809763, |
|
|
676 |
0.7200961165080368, |
|
|
677 |
0.9999997373138294, |
|
|
678 |
0.5115953505542589, |
|
|
679 |
0.9999997373138294, |
|
|
680 |
0.845756654704669, |
|
|
681 |
0.5676481671711865, |
|
|
682 |
0.8395655047552425, |
|
|
683 |
0.36422621419559664, |
|
|
684 |
0.9999997373138294, |
|
|
685 |
0.9999997373138294, |
|
|
686 |
0.9239752719474906, |
|
|
687 |
0.9999997373138294, |
|
|
688 |
0.2321774685303417, |
|
|
689 |
0.5115953505542589, |
|
|
690 |
0.9239752719474906, |
|
|
691 |
0.5070330046729763, |
|
|
692 |
0.09174034333551025, |
|
|
693 |
0.9999997373138294, |
|
|
694 |
0.9999997373138294, |
|
|
695 |
0.9999997373138294, |
|
|
696 |
0.7200961165080368, |
|
|
697 |
0.9999997373138294, |
|
|
698 |
0.9999997373138294, |
|
|
699 |
0.9999997373138294, |
|
|
700 |
0.6847287526005329, |
|
|
701 |
0.9999997373138294, |
|
|
702 |
0.5442138166006407, |
|
|
703 |
0.9999997373138294, |
|
|
704 |
0.9999997373138294, |
|
|
705 |
0.9999997373138294, |
|
|
706 |
0.9658912215110148, |
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0.5892132685871182, |
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0.9999997373138294, |
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0.9999997373138294, |
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0.8063836512383536, |
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0.9999997373138294, |
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0.3635268253933128, |
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0.878906678789298, |
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0.9999997373138294, |
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0.845756654704669, |
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0.9999997373138294, |
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0.02353676743785122, |
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0.9999997373138294, |
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0.4372483768805375, |
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0.6899654596418524, |
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0.9239752719474906, |
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0.5115953505542589, |
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0.9999997373138294, |
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0.9999997373138294, |
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0.19158373821572414, |
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0.9999997373138294, |
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0.6681718367617152, |
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0.7139678179747181, |
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0.9999997373138294, |
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0.14361191965472642, |
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0.5626777439383062, |
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0.9999997373138294, |
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0.5115953505542589, |
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0.9999997373138294, |
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0.9999997373138294, |
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0.9999997373138294, |
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0.8395655047552425, |
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0.6847287526005329, |
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0.9999997373138294, |
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0.6847287526005329, |
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0.9999997373138294, |
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0.45397729003343607, |
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0.19266295410826276, |
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0.9999997373138294, |
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0.6847287526005329, |
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0.5274203426647385, |
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0.33573852446575575, |
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0.9999997373138294, |
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0.5115953505542589, |
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0.01737015553722674, |
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0.9999997373138294, |
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0.845756654704669, |
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0.5306621528598132, |
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0.13720519336046125, |
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0.014432955706249317, |
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0.9999997373138294, |
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0.29234617948435815, |
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0.9999997373138294, |
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0.18171356404052635, |
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0.9550708068178158, |
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0.45143711607921805, |
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0.9999997373138294, |
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0.04693144675687698, |
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0.8395655047552425, |
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0.8395655047552425, |
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0.9999997373138294, |
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0.8395655047552425, |
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0.9999997373138294, |
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0.7223703085727059, |
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0.02353676743785122, |
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0.19266295410826276, |
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0.4993454158594806, |
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0.9999997373138294, |
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0.878906678789298, |
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0.5115953505542589, |
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0.9999997373138294, |
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0.29234617948435815, |
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0.9999997373138294, |
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0.9999997373138294, |
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0.19266295410826276, |
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0.9999997373138294, |
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0.9999997373138294, |
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833 |
0.7200961165080368, |
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0.9999997373138294, |
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0.03371060943211578, |
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0.7200961165080368, |
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0.9999997373138294, |
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0.7200961165080368, |
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0.9550708068178158, |
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840 |
0.18171356404052635, |
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841 |
0.9999997373138294, |
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842 |
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0.9999997373138294, |
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0.7200961165080368, |
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0.9999997373138294, |
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846 |
0.9850862188123334, |
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847 |
0.9999997373138294, |
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848 |
0.04693144675687698, |
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849 |
0.19266295410826276, |
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850 |
0.9999997373138294, |
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851 |
0.9999997373138294, |
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852 |
0.9999997373138294, |
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853 |
0.8280732314616722, |
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|
854 |
0.9327511393735692, |
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855 |
0.9999997373138294, |
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|
856 |
0.9999997373138294, |
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857 |
0.9999997373138294, |
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858 |
0.5115953505542589, |
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859 |
0.9999997373138294, |
|
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860 |
0.9999997373138294, |
|
|
861 |
], |
|
|
862 |
}, |
|
|
863 |
index=[f"gene{i}" for i in range(200)], |
|
|
864 |
) |
|
|
865 |
pd.testing.assert_frame_equal(res, ref, rtol=1e-4) |
|
|
866 |
|
|
|
867 |
def test_meta_de_nan(self): |
|
|
868 |
"""check robustness of meta_de to NaN values""" |
|
|
869 |
idx = ["gene1", "gene2", "gene3"] |
|
|
870 |
res1 = DEResults( |
|
|
871 |
{ |
|
|
872 |
"log2FoldChange": [1.0, np.nan, 3.0], |
|
|
873 |
"lfcSE": [0.5, np.nan, 0.5], |
|
|
874 |
"pvalue": [0.1, np.nan, 0.2], |
|
|
875 |
}, |
|
|
876 |
index=idx, |
|
|
877 |
) |
|
|
878 |
res2 = DEResults( |
|
|
879 |
{ |
|
|
880 |
"log2FoldChange": [2.0, 3.0, 4.0], |
|
|
881 |
"lfcSE": [0.5, 0.5, 0.5], |
|
|
882 |
"pvalue": [0.1, 0.15, 0.2], |
|
|
883 |
}, |
|
|
884 |
index=idx, |
|
|
885 |
) |
|
|
886 |
res3 = DEResults( |
|
|
887 |
{ |
|
|
888 |
"log2FoldChange": [3.0, np.nan, 5.0], |
|
|
889 |
"lfcSE": [0.5, np.nan, 0.5], |
|
|
890 |
"pvalue": [0.2, np.nan, 0.1], |
|
|
891 |
}, |
|
|
892 |
index=idx, |
|
|
893 |
) |
|
|
894 |
meta1 = meta_de([res1, res2, res3]) |
|
|
895 |
meta2 = meta_de([res1, res3]) |
|
|
896 |
ref1 = pd.DataFrame( |
|
|
897 |
{ |
|
|
898 |
"combined logFC (CI_L)": [ |
|
|
899 |
0.8684142716330685, |
|
|
900 |
np.nan, |
|
|
901 |
2.868414271633068, |
|
|
902 |
], |
|
|
903 |
"combined logFC (CI_R)": [ |
|
|
904 |
3.1315857283669315, |
|
|
905 |
np.nan, |
|
|
906 |
5.131585728366931, |
|
|
907 |
], |
|
|
908 |
"combined logFC": [2, np.nan, 4], |
|
|
909 |
"adjusted combined pval": [ |
|
|
910 |
0.13058835750961412, |
|
|
911 |
0.15, |
|
|
912 |
0.13058835750961412, |
|
|
913 |
], |
|
|
914 |
}, |
|
|
915 |
index=idx, |
|
|
916 |
) |
|
|
917 |
ref2 = pd.DataFrame( |
|
|
918 |
{ |
|
|
919 |
"combined logFC (CI_L)": [ |
|
|
920 |
0.0400360524639638, |
|
|
921 |
np.nan, |
|
|
922 |
2.0400360524639636, |
|
|
923 |
], |
|
|
924 |
"combined logFC (CI_R)": [ |
|
|
925 |
3.9599639475360364, |
|
|
926 |
np.nan, |
|
|
927 |
5.959963947536036, |
|
|
928 |
], |
|
|
929 |
"combined logFC": [2, np.nan, 4], |
|
|
930 |
"adjusted combined pval": [ |
|
|
931 |
0.09824046010856295, |
|
|
932 |
np.nan, |
|
|
933 |
0.09824046010856295, |
|
|
934 |
], |
|
|
935 |
}, |
|
|
936 |
index=idx, |
|
|
937 |
) |
|
|
938 |
pd.testing.assert_frame_equal(meta1, ref1) |
|
|
939 |
pd.testing.assert_frame_equal(meta2, ref2) |