import unittest
import numpy as np
from inmoose.deseq2 import makeExampleDESeqDataSet, varianceStabilizingTransformation
class Test(unittest.TestCase):
def test_varianceStabilizingTransform(self):
"""check that variance StabilizingTransform works as expected"""
dds = makeExampleDESeqDataSet(n=15, m=12, seed=42)
vst = varianceStabilizingTransformation(dds)
ref = np.array(
[
[
3.823017,
3.8230169,
5.985321,
4.913315,
4.161231,
1.494246,
4.823440,
5.450071,
3.823017,
1.3401978,
3.595272,
3.823017,
],
[
-0.451858,
0.6581684,
2.810054,
1.254434,
-0.451858,
4.077032,
-0.451858,
-0.451858,
4.086414,
-0.4518580,
1.546176,
2.955590,
],
[
8.061588,
6.3072368,
4.637324,
1.851704,
4.161231,
7.255872,
0.824648,
5.171055,
5.671037,
5.1710549,
5.919773,
8.977944,
],
[
4.243021,
6.7404002,
6.359506,
2.576007,
5.365497,
5.015233,
2.906480,
8.951864,
4.671504,
5.9054920,
6.892472,
5.308661,
],
[
2.178302,
-0.4518580,
1.105434,
-0.451858,
1.395415,
-0.451858,
-0.451858,
3.694642,
3.500141,
0.6253966,
3.595272,
-0.451858,
],
[
2.955590,
-0.4518580,
-0.451858,
2.576007,
1.847902,
1.494246,
0.824648,
3.183966,
3.500141,
1.3401978,
3.135366,
4.359573,
],
[
-0.451858,
3.3285650,
1.664144,
2.261056,
1.641409,
2.586723,
4.623337,
6.141930,
-0.451858,
-0.4518580,
2.834227,
6.598715,
],
[
4.359573,
2.0207666,
4.118937,
1.851704,
4.233253,
2.920369,
-0.451858,
3.183966,
2.057386,
1.0399000,
1.012888,
4.359573,
],
[
2.178302,
-0.4518580,
-0.451858,
6.038225,
5.755725,
3.416888,
2.327658,
3.183966,
3.082433,
3.9153624,
5.408736,
-0.451858,
],
[
3.226560,
3.2613786,
2.992774,
3.553961,
2.184300,
1.494246,
0.824648,
-0.451858,
-0.451858,
1.0399000,
3.264959,
-0.451858,
],
[
5.249530,
1.0834807,
2.992774,
3.925805,
4.896815,
6.210543,
4.823440,
6.519649,
5.630417,
-0.4518580,
4.875050,
7.268652,
],
[
4.749485,
4.3272243,
4.791961,
5.117967,
2.962466,
4.791961,
4.791961,
4.367923,
6.588150,
5.6595787,
4.791961,
4.749485,
],
[
5.472762,
2.3195612,
3.154617,
3.688910,
4.896815,
4.791961,
4.163592,
3.183966,
2.816266,
3.1140628,
1.012888,
6.972229,
],
[
3.650416,
4.1161861,
4.335770,
6.507277,
6.111061,
8.069817,
5.319135,
5.736698,
5.786454,
-0.4518580,
7.342527,
7.587853,
],
[
4.910890,
1.6362631,
4.690736,
6.817270,
1.847902,
6.556714,
3.832819,
3.694642,
-0.451858,
4.9890014,
2.210771,
4.116186,
],
]
)
self.assertTrue(np.allclose(vst.X, ref.T, atol=2e-2))
ref = np.array(
[
[
3.701496,
3.7014964,
5.958395,
4.8565583,
4.0653149,
0.8610695,
4.7630157,
5.411009,
3.701496,
0.6327990,
3.4527199,
3.701496,
],
[
-2.822746,
-0.4959506,
2.562285,
0.5019767,
-2.8227460,
3.9753014,
-2.8227460,
-2.822746,
3.985348,
-2.8227460,
0.9362035,
2.732023,
],
[
8.055215,
6.2857065,
4.568530,
1.3618038,
4.0653149,
7.2447271,
-0.2002053,
5.123623,
5.637539,
5.1236227,
5.8915925,
8.974568,
],
[
4.152433,
6.7244620,
6.338743,
2.2835920,
5.3240677,
4.9623662,
2.6750276,
8.948426,
4.604330,
5.8770306,
6.8781302,
5.265561,
],
[
1.790356,
-2.8227460,
0.267767,
-2.8227460,
0.7155806,
-2.8227460,
-2.8227460,
3.561685,
3.347746,
-0.5558881,
3.4527199,
-2.822746,
],
[
2.732023,
-2.8227460,
-2.822746,
2.2835920,
1.3566659,
0.8610695,
-0.2002053,
2.993639,
3.347746,
0.6327990,
2.9384128,
4.276066,
],
[
-2.822746,
3.1566484,
1.103729,
1.8953193,
1.0717726,
2.2965211,
4.5538679,
6.117780,
-2.822746,
-2.8227460,
2.5906548,
6.581130,
],
[
4.276066,
1.5866643,
4.020143,
1.3618038,
4.1420452,
2.6911747,
-2.8227460,
2.993639,
1.634489,
0.1617874,
0.1175492,
4.276066,
],
[
1.790356,
-2.8227460,
-2.822746,
6.0122710,
5.7241411,
3.2553183,
1.9788499,
2.993639,
2.877997,
3.8014500,
5.3685344,
-2.822746,
],
[
3.041855,
3.0811437,
2.774996,
3.4072156,
1.7980092,
0.8610695,
-0.2002053,
-2.822746,
-2.822746,
0.1617874,
3.0851780,
-2.822746,
],
[
5.204619,
0.2324742,
2.774996,
3.8127224,
4.8394025,
6.1875168,
4.7630157,
6.501071,
5.595959,
-2.8227460,
4.8167596,
7.257606,
],
[
4.685865,
4.2418104,
4.730196,
5.0687489,
2.7399816,
4.7301962,
4.7301962,
4.284902,
6.570435,
5.6258120,
4.7301962,
4.685865,
],
[
5.434311,
1.9687389,
2.960316,
3.5554177,
4.8394025,
4.7301962,
4.0678339,
2.993639,
2.569582,
2.9141319,
0.1175492,
6.958660,
],
[
3.513271,
4.0172023,
4.250864,
6.4885385,
6.0863872,
8.0634801,
5.2763471,
5.704694,
5.755538,
-2.8227460,
7.3320319,
7.579001,
],
[
4.854038,
1.0645175,
4.624456,
6.8021604,
1.3566659,
6.5386078,
3.7121294,
3.561685,
-2.822746,
4.9351593,
1.8316982,
4.017202,
],
]
)
dds = makeExampleDESeqDataSet(n=15, m=12, seed=42)
vst = varianceStabilizingTransformation(dds, fitType="mean")
self.assertTrue(np.allclose(vst.X, ref.T, atol=3e-2))
Datasets
Models
