首页下载资源大数据PRScs源代码详解以及代码步骤测试

ZIPPRScs源代码详解以及代码步骤测试

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资源文件列表:

PRScs.zip 大约有14个文件
  1. PRScs/
  2. PRScs/PRScs.ipynb 8.59KB
  3. PRScs/PRScs_test.ipynb 4.01KB
  4. PRScs/gigrnd.ipynb 14.16KB
  5. PRScs/mcmc_gtb.ipynb 16.69KB
  6. PRScs/mcmc_gtb_test.ipynb 17.93KB
  7. PRScs/parse_genet.ipynb 12.77KB
  8. PRScs/parse_genet_test.ipynb 32.8KB
  9. PRScs/res/
  10. PRScs/test_data/
  11. PRScs/test_data/sumstats.txt 35.46KB
  12. PRScs/test_data/sumstats_pval.txt 35.46KB
  13. PRScs/test_data/sumstats_se.txt 35.46KB
  14. PRScs/test_data/test.bim 27.18KB

资源介绍:

PRScs 是一种用于计算多性状基因风险评分（Polygenic Risk Scores, PRS）的方法，特别适用于全基因组关联分析（GWAS）数据。PRScs 是 Polygenic Risk Score - Continuous Shrinkage 的缩写，它的主要特点是在计算 PRS 时引入了连续收缩（continuous shrinkage）模型，从而对多种基因变异进行联合分析。 PRScs 的主要特点包括： 1.贝叶斯模型： PRScs 基于贝叶斯框架，使用连续收缩先验（continuous shrinkage prior），能够动态地调整每个 SNP 的权重，从而优化 PRS 的计算。传统的 PRS 方法通常假设所有 SNP 贡献相同，而 PRScs 可以根据数据对 SNP 贡献进行加权。 2. 利用外部信息： PRScs 允许使用外部信息（如 LD 参考面板）来提高 PRS 的预测能力。LD 参考面板可以是来自相同或不同人群的基因数据，这可以帮助更好地捕捉 SNP 之间的连锁不平衡（LD）结构。
SNP A1 A2 BETA SE rs9605903 T C -0.011400 8.117350e-03 rs5746647 G T -0.007900 1.506482e-02 rs5747999 C A -0.006000 8.780564e-03 rs2845380 A G 0.010700 7.281439e-03 rs2247281 G A 0.011700 6.950269e-03 rs2845346 C T 0.010700 8.055794e-03 rs2845347 C T 0.010900 8.081235e-03 rs1807512 T C 0.015700 7.313244e-03 rs5748593 T C 0.014900 8.006321e-03 rs9606468 T C -0.000100 8.141474e-03 rs4819535 T C -0.014100 1.285481e-02 rs5748648 G A -0.015600 1.332198e-02 rs738045 G A -0.002600 6.719373e-03 rs7284996 T C -0.002400 6.794029e-03 rs2385714 T C -0.000400 6.874436e-03 rs2080203 T G 0.001300 7.302171e-03 rs2072466 C T 0.016300 8.696611e-03 rs9605155 G T 0.007300 6.232680e-03 rs874835 A G 0.007200 6.257647e-03 rs874836 A G 0.007800 8.879284e-03 rs5994031 C T 0.001700 6.383523e-03 rs2215842 C T 0.001200 6.186549e-03 rs2192431 T G -0.012500 9.361660e-03 rs175138 G A 0.001600 6.112273e-03 rs175139 C T 0.001700 6.389754e-03 rs983305 G A 0.007000 6.251129e-03 rs9606478 G A 0.012500 7.083495e-03 rs175140 T G -0.014200 9.317372e-03 rs1860944 G A 0.007100 6.254516e-03 rs175145 A G 0.006900 9.162336e-03 rs175147 G T 0.001400 6.481953e-03 rs16981741 A G 0.002300 7.000574e-03 rs165652 T G -0.011100 7.494811e-03 rs165757 G A -0.010800 7.491395e-03 rs175152 A C -0.011000 7.545698e-03 rs165778 T C -0.013900 7.943691e-03 rs165810 C A -0.011200 6.278814e-03 rs2075120 C T 0.004400 7.231686e-03 rs175154 A G -0.012000 7.844862e-03 rs165808 C T -0.012800 7.909581e-03 rs165890 T C -0.012000 7.863492e-03 rs2041608 T G -0.018300 2.498498e-02 rs12169910 C T -0.018700 2.496346e-02 rs165886 G A -0.011000 7.714478e-03 rs165698 T C -0.011800 7.730399e-03 rs165608 G A -0.010800 6.235292e-03 rs165790 T C -0.011700 7.751493e-03 rs7291500 T G -0.023900 2.564716e-02 rs16981833 C T -0.012700 1.488362e-02 rs7288841 C T -0.003700 8.702043e-03 rs9606534 T C -0.005600 8.763210e-03 rs7293026 T C 0.004400 8.057192e-03 rs8136206 C A 0.001700 9.019501e-03 rs5992587 C T -0.007800 7.018231e-03 rs11703901 C T 0.021400 9.072088e-03 rs2003568 T C 0.000001 1.000000e+00 rs12485066 G A 0.020900 1.051061e-02 rs5992589 G A -0.004600 7.378499e-03 rs9306242 A G -0.004200 7.467146e-03 rs9605179 A G 0.011600 6.892346e-03 rs9618937 G A -0.004900 6.599555e-03 rs17806382 G A -0.009500 1.396720e-02 rs5748748 T C -0.009000 1.017468e-02 rs5748752 C T -0.007900 7.205343e-03 rs5748755 C T -0.006300 7.143204e-03 rs2385785 G A -0.006800 9.887080e-03 rs933461 G A -0.006500 7.121722e-03 rs1981707 T C 0.007300 7.661765e-03 rs17733785 T C 0.002600 9.725094e-03 rs8137298 A C 0.010200 9.336124e-03 rs11914017 T C 0.003100 9.597710e-03 rs11089387 T C 0.004700 6.610644e-03 rs5992598 C T 0.009200 9.295347e-03 rs7287116 T C 0.008800 9.314894e-03 rs1024732 G A -0.010100 6.595786e-03 rs5748765 A C -0.010100 6.429332e-03 rs5748766 T G 0.009300 9.263358e-03 rs4819925 C T -0.004400 7.074961e-03 rs2041607 G A -0.010700 6.562483e-03 rs759076 G A -0.004800 6.979115e-03 rs757630 T C -0.003500 7.746480e-03 rs4819934 G A 0.002700 1.042287e-02 rs4819936 G A 0.003600 1.063989e-02 rs5992604 G A -0.008800 6.498714e-03 rs11913227 T C -0.003600 1.067758e-02 rs917838 T C -0.003600 7.449164e-03 rs738031 G T 0.012200 1.318464e-02 rs4141523 G T 0.003900 9.208064e-03 rs5748829 A G -0.015300 1.208229e-02 rs928831 T C 0.004000 1.023028e-02 rs2845394 A G 0.005500 6.486701e-03 rs2845393 T G 0.004600 6.394297e-03 rs16981964 T C -0.016400 1.196557e-02 rs9606592 T G 0.003800 6.377837e-03 rs5748845 C T -0.017800 1.195167e-02 rs5994155 C A 0.003900 8.011502e-03 rs5748850 T G 0.004900 7.976223e-03 rs2041629 A G 0.004100 7.900664e-03 rs4819956 A C -0.002400 7.093262e-03 rs4819553 G A 0.003000 8.076387e-03 rs4819958 A G 0.003000 8.027035e-03 rs4819554 G A 0.003000 7.975388e-03 rs2241042 A C 0.000700 6.542905e-03 rs2241043 C T 0.000400 6.830225e-03 rs2241044 A C -0.003300 6.641942e-03 rs2241046 C T -0.003100 7.439457e-03 rs879577 C T 0.000500 7.550206e-03 rs879575 C T 0.001200 7.424526e-03 rs738034 G A -0.000700 6.566114e-03 rs3827278 C A -0.006100 7.654511e-03 rs1047929 T C 0.006000 7.048004e-03 rs7289082 A G 0.006600 7.100149e-03 rs12170331 G A 0.007400 7.116270e-03 rs974396 A G 0.016900 1.313734e-02 rs738033 G T 0.005900 7.085175e-03 rs2277830 A C 0.023000 1.532882e-02 rs3827295 G A 0.014600 1.432176e-02 rs5748875 T C 0.012500 7.704242e-03 rs5747004 C A 0.015500 1.356256e-02 rs4819558 C T -0.000600 7.789214e-03 rs4819559 A C -0.001700 8.082039e-03 rs5994175 G T -0.006300 7.212506e-03 rs740422 C T 0.004500 8.207493e-03 rs1034859 C A -0.006600 6.737672e-03 rs3788269 G A 0.003000 2.086995e-02 rs5994180 A G 0.013600 1.522456e-02 rs5994186 G A -0.008700 7.070144e-03 rs5994187 G A -0.008200 7.078717e-03 rs5748919 C T -0.008200 7.059259e-03 rs1125471 C A -0.001800 7.634094e-03 rs1076102 A G 0.006300 6.771787e-03 rs1135909 T C 0.012900 7.692719e-03 rs3171599 A G 0.016300 7.458611e-03 rs1139056 A G 0.015800 7.360256e-03 rs2231495 T C -0.012300 8.138434e-03 rs17807317 A C 0.004000 6.703407e-03 rs1076106 C A 0.003200 8.434644e-03 rs362129 G A 0.006400 6.754841e-03 rs5748954 T C 0.000200 5.179781e-03 rs737967 C T 0.004400 6.318521e-03 rs5748965 T C 0.002100 6.435863e-03 rs5748966 C T 0.004400 6.304054e-03 rs5994213 G A 0.002400 7.325590e-03 rs5747033 A G -0.002900 1.935548e-02 rs5748972 G A 0.008000 1.787078e-02 rs5747037 G A -0.013500 7.563774e-03 rs9605246 T C 0.012100 1.100845e-02 rs5994231 T C -0.006900 9.652337e-03 rs5749002 G A 0.003400 1.308581e-02 rs5749011 T C -0.012900 1.269083e-02 rs11704699 T G -0.008600 1.173632e-02 rs8140080 G A -0.003000 7.483321e-03 rs4819994 T C -0.003800 7.404285e-03 rs5747058 G A 0.009900 6.420686e-03 rs5749016 C T 0.010800 6.388794e-03 rs12160031 G A 0.001800 9.201056e-03 rs9605252 C T 0.015200 8.713043e-03 rs4819996 A G 0.003500 7.246467e-03 rs9606682 T C 0.005900 7.270821e-03 rs5994254 G A -0.009200 2.150560e-02 rs5994256 T C 0.005000 7.585537e-03 rs9605258 T G 0.000500 6.178407e-03 rs9605259 T C 0.004100 7.790664e-03 rs9306256 C T 0.004300 8.699312e-03 rs9619055 C T 0.000100 5.502349e-03 rs9306258 G A 0.005000 8.774706e-03 rs5994258 A G -0.000700 6.934978e-03 rs5994260 A G 0.004200 9.077719e-03 rs9617984 C T -0.001600 7.023637e-03 rs17808489 G A -0.009400 9.671771e-03 rs5992665 A G -0.008800 7.345308e-03 rs5994271 G A 0.007400 6.866937e-03 rs2040692 C T -0.001900 6.091271e-03 rs7288834 G T -0.003700 6.418414e-03 rs4607032 G T -0.002200 7.158668e-03 rs5992674 T C 0.026100 1.093160e-02 rs5992034 G T 0.029500 1.107362e-02 rs9618000 A G 0.019900 1.021977e-02 rs5746359 C T 0.009200 1.527957e-02 rs4819447 T G -0.039900 2.173061e-02 rs16982354 G A -0.023200 3.398300e-02 rs5747103 C T 0.005900 6.658898e-03 rs1860309 G A 0.003900 6.623718e-03 rs5746366 A G 0.006100 6.524223e-03 rs5747112 G A 0.005900 6.527973e-03 rs16982402 T C -0.013100 9.851461e-03 rs2078734 C T -0.007600 6.283983e-03 rs1859120 A G -0.003600 7.053859e-03 rs5747122 A C -0.050100 3.156789e-02 rs12628081 A G -0.056300 3.150777e-02 rs5746373 T C -0.053000 3.168469e-02 rs2895937 A G -0.004000 8.671582e-03 rs1981533 T G 0.003600 7.004827e-03 rs2189077 T C 0.006900 8.055680e-03 rs5747132 C T 0.004100 8.191272e-03 rs5992705 C A 0.010500 2.109130e-02 rs5992707 A G 0.006400 2.086982e-02 rs5746398 T C 0.007800 9.230557e-03 rs5747164 T G 0.007900 9.199836e-03 rs1004973 G A 0.007700 9.217288e-03 rs12157361 C T 0.002600 1.220459e-02 rs5747183 A G -0.006300 1.229950e-02 rs2522288 T C 0.001200 1.106003e-02 rs5747187 C T 0.010100 1.306819e-02 rs4819591 C T 0.009100 1.203839e-02 rs17741035 T C 0.027900 2.448985e-02 rs5746415 A G 0.012200 1.342554e-02 rs5747195 A G 0.012200 1.338643e-02 rs2522297 T C 0.001900 6.895505e-03 rs7288509 A G -0.008500 8.408969e-03 rs1296754 G A 0.007700 8.000025e-03 rs4819594 T C 0.001700 8.452410e-03 rs9605311 G A 0.002100 8.537382e-03 rs8141657 A G 0.006400 6.959811e-03 rs5747211 G A -0.004500 9.886810e-03 rs174301 T C 0.001600 7.975494e-03 rs174306 A G 0.003600 6.585230e-03 rs174313 G T 0.002700 6.622651e-03 rs174330 T C -0.001900 7.647961e-03 rs2401125 T G 0.001900 7
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