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Merge pull request #161 from mgalardini/wg_lineage
Fix elastic net with lineages
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'''Python reimplementation of SEER for bacterial GWAS''' | ||
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__version__ = '1.3.8' | ||
__version__ = '1.3.9' |
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variant af filter-pvalue lrt-pvalue beta beta-std-err intercept PC1 PC2 PC3 notes | ||
CDS1 8.00E-02 8.01E-01 1.00E+00 -4.57E-01 9.97E-01 2.75E-01 -9.90E-01 -3.91E-01 4.33E-01 bad-chisq | ||
CDS2 1.40E-01 4.50E-01 1.00E+00 -8.47E-02 1.31E+00 2.51E-01 -9.13E-01 -3.30E-01 4.53E-01 bad-chisq | ||
CDS3 2.20E-01 4.25E-01 6.99E-01 -3.25E-01 8.40E-01 3.29E-01 -9.59E-01 -4.28E-01 5.52E-01 | ||
variant af filter-pvalue lrt-pvalue beta notes | ||
FM211187_184_G_A 4.00E-02 2.01E-01 3.40E-01 NA bad-chisq | ||
FM211187_293_G_A 2.00E-02 2.54E-01 -6.69E-01 NA bad-chisq | ||
FM211187_869_C_T 1.00E-01 7.84E-03 -1.63E+00 NA bad-chisq | ||
FM211187_926_G_A 2.00E-02 2.54E-01 -8.91E-05 NA bad-chisq | ||
FM211187_1981_G_A 9.40E-01 1.13E-01 2.66E-02 NA bad-chisq | ||
FM211187_2032_C_A 2.00E-02 2.54E-01 -6.78E-01 NA bad-chisq | ||
FM211187_2865_C_T 2.00E-02 2.54E-01 -4.09E-05 NA bad-chisq | ||
FM211187_2943_T_C 1.20E-01 2.06E-02 1.44E+00 NA bad-chisq | ||
FM211187_3982_C_A 4.00E-02 2.01E-01 1.39E-01 NA bad-chisq | ||
FM211187_6054_C_T 6.00E-02 1.13E-01 4.74E-03 NA bad-chisq | ||
FM211187_6139_A_G 2.00E-02 2.54E-01 -4.40E-02 NA bad-chisq | ||
FM211187_7799_C_T 4.00E-02 2.01E-01 2.46E-04 NA bad-chisq | ||
FM211187_8872_A_G 2.40E-01 2.51E-01 -1.29E-02 NA | ||
FM211187_10838_C_T 5.20E-01 1.64E-01 -4.50E-01 NA | ||
FM211187_11527_T_C 4.80E-01 1.64E-01 -2.77E-01 NA | ||
FM211187_11559_T_G 4.00E-02 2.01E-01 8.47E-05 NA bad-chisq | ||
FM211187_11633_A_G 2.00E-02 2.54E-01 -2.81E-03 NA bad-chisq | ||
FM211187_11762_G_T 6.00E-02 1.13E-01 3.16E-03 NA bad-chisq | ||
FM211187_12304_C_CTTATA 2.00E-02 3.71E-01 7.90E-01 NA bad-chisq | ||
FM211187_13550_G_A 4.00E-02 2.01E-01 9.41E-06 NA bad-chisq | ||
FM211187_13781_C_T 2.00E-02 2.54E-01 -1.02E-04 NA bad-chisq | ||
FM211187_14044_G_A 3.00E-01 1.06E-01 5.63E-01 NA |
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Read 50 phenotypes | ||
Detected binary phenotype | ||
Loaded projection with dimension (50, 35) | ||
Analysing 50 samples found in both phenotype and structure matrix | ||
3 loaded variants | ||
0 pre-filtered variants | ||
3 tested variants | ||
3 printed variants |
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Original file line number | Diff line number | Diff line change |
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variant af filter-pvalue lrt-pvalue beta beta-std-err intercept PC1 PC2 PC3 notes | ||
CDS1 8.00E-02 8.01E-01 1.00E+00 -4.57E-01 9.97E-01 2.75E-01 -9.90E-01 -3.91E-01 4.33E-01 bad-chisq | ||
CDS2 1.40E-01 4.50E-01 1.00E+00 -8.47E-02 1.31E+00 2.51E-01 -9.13E-01 -3.30E-01 4.53E-01 bad-chisq | ||
CDS3 2.20E-01 4.25E-01 6.99E-01 -3.25E-01 8.40E-01 3.29E-01 -9.59E-01 -4.28E-01 5.52E-01 |
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