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| author | Alexander Kabui | 2021-03-16 11:38:13 +0300 |
|---|---|---|
| committer | GitHub | 2021-03-16 11:38:13 +0300 |
| commit | 56ce88ad31dec3cece63e9370ca4e4c02139753b (patch) | |
| tree | 766504dfaca75a14cc91fc3d88c41d1e775d415f /tests/integration/expected_corr_results.json | |
| parent | 43d1bb7f6cd2b5890d5b3eb7c357caafda25a35c (diff) | |
| download | genenetwork3-56ce88ad31dec3cece63e9370ca4e4c02139753b.tar.gz | |
delete unwanted correlation stuff (#5)
* delete unwanted correlation stuff
* Refactor/clean up correlations (#4)
* initial commit for Refactor/clean-up-correlation
* add python scipy dependency
* initial commit for sample correlation
* initial commit for sample correlation endpoint
* initial commit for integration and unittest
* initial commit for registering correlation blueprint
* add and modify unittest and integration tests for correlation
* Add compute compute_all_sample_corr method for correlation
* add scipy to requirement txt file
* add tissue correlation for trait list
* add unittest for tissue correlation
* add lit correlation for trait list
* add unittests for lit correlation for trait list
* modify lit correlarion for trait list
* add unittests for lit correlation for trait list
* add correlation metho in dynamic url
* add file format for expected structure input while doing sample correlation
* modify input data structure -> add trait id
* update tests for sample r correlation
* add compute all lit correlation method
* add endpoint for computing lit_corr
* add unit and integration tests for computing lit corr
* add /api/correlation/tissue_corr/{corr_method} endpoint for tissue correlation
* add unittest and integration tests for tissue correlation
Co-authored-by: BonfaceKilz <bonfacemunyoki@gmail.com>
* update guix scm file
* fix pylint error for correlations api
Co-authored-by: BonfaceKilz <bonfacemunyoki@gmail.com>
Diffstat (limited to 'tests/integration/expected_corr_results.json')
| -rw-r--r-- | tests/integration/expected_corr_results.json | 1902 |
1 files changed, 0 insertions, 1902 deletions
diff --git a/tests/integration/expected_corr_results.json b/tests/integration/expected_corr_results.json deleted file mode 100644 index b5bbc2d..0000000 --- a/tests/integration/expected_corr_results.json +++ /dev/null @@ -1,1902 +0,0 @@ -[ - { - "index": 1, - "trait_id": "1415758_at", - "dataset": "HC_M2_0606_P", - "hmac": "1415758_at:HC_M2_0606_P:da50fa1141a7d608ab20", - "symbol": "Fryl", - "description": "furry homolog-like; far 3' UTR", - "location": "Chr5: 72.964984", - "mean": "9.193", - "additive": "-0.081", - "lod_score": "4.4", - "lrs_location": "Chr1: 196.404284", - "sample_r": "-0.407", - "num_overlap": 67, - "sample_p": "6.234e-04", - "lit_corr": "--", - "tissue_corr": "-0.221", - "tissue_pvalue": "2.780e-01" - }, - { - "index": 2, - "trait_id": "1415693_at", - "dataset": "HC_M2_0606_P", - "hmac": "1415693_at:HC_M2_0606_P:0959e913366f559ea22b", - "symbol": "Derl1", - "description": "derlin 1; proximal to mid 3' UTR", - "location": "Chr15: 57.702171", - "mean": "9.445", - "additive": "0.056", - "lod_score": "2.1", - "lrs_location": "Chr1: 193.731996", - "sample_r": "0.398", - "num_overlap": 67, - "sample_p": "8.614e-04", - "lit_corr": "--", - "tissue_corr": "0.114", - "tissue_pvalue": "5.800e-01" - }, - { - "index": 3, - "trait_id": "1415753_at", - "dataset": "HC_M2_0606_P", - "hmac": "1415753_at:HC_M2_0606_P:d75ca42e7fa1613364bb", - "symbol": "Fam108a", - "description": "abhydrolase domain-containing protein FAM108A; last two exons and proximal 3' UTR", - "location": "Chr10: 80.046470", - "mean": "12.731", - "additive": "0.050", - "lod_score": "1.5", - "lrs_location": "ChrX: 103.404884", - "sample_r": "0.384", - "num_overlap": 67, - "sample_p": "1.344e-03", - "lit_corr": "--", - "tissue_corr": "0.108", - "tissue_pvalue": "5.990e-01" - }, - { - "index": 4, - "trait_id": "1415740_at", - "dataset": "HC_M2_0606_P", - "hmac": "1415740_at:HC_M2_0606_P:755cdc41d0d50a03b647", - "symbol": "Psmc5", - "description": "protease (prosome, macropain) 26S subunit, ATPase 5; exons 7, 8, 9", - "location": "Chr11: 106.123450", - "mean": "12.424", - "additive": "0.059", - "lod_score": "2.6", - "lrs_location": "Chr9: 34.013550", - "sample_r": "0.364", - "num_overlap": 67, - "sample_p": "2.476e-03", - "lit_corr": "--", - "tissue_corr": "0.333", - "tissue_pvalue": "9.696e-02" - }, - { - "index": 5, - "trait_id": "1415757_at", - "dataset": "HC_M2_0606_P", - "hmac": "1415757_at:HC_M2_0606_P:8bbf06aa2e3aa5530934", - "symbol": "Gbf1", - "description": "Golgi-specific brefeldin A-resistance factor 1; last exon and proximal 3' UTR", - "location": "Chr19: 46.360410", - "mean": "9.800", - "additive": "-0.062", - "lod_score": "2.0", - "lrs_location": "Chr17: 52.750885", - "sample_r": "0.363", - "num_overlap": 67, - "sample_p": "2.539e-03", - "lit_corr": "--", - "tissue_corr": "-0.059", - "tissue_pvalue": "7.741e-01" - }, - { - "index": 6, - "trait_id": "1415768_a_at", - "dataset": "HC_M2_0606_P", - "hmac": "1415768_a_at:HC_M2_0606_P:5e67109eee04f5da3393", - "symbol": "Ube2r2", - "description": "ubiquitin-conjugating enzyme E2R 2", - "location": "Chr4: 41.137929", - "mean": "9.811", - "additive": "-0.087", - "lod_score": "3.3", - "lrs_location": "Chr12: 114.553844", - "sample_r": "-0.312", - "num_overlap": 67, - "sample_p": "1.019e-02", - "lit_corr": "--", - "tissue_corr": "-0.007", - "tissue_pvalue": "9.711e-01" - }, - { - "index": 7, - "trait_id": "1415670_at", - "dataset": "HC_M2_0606_P", - "hmac": "1415670_at:HC_M2_0606_P:4f82d7374f29ebfacaaf", - "symbol": "Copg", - "description": "coatomer protein complex, subunit gamma 1; two of the three last exons and proximal 3' UTR", - "location": "Chr6: 87.859681", - "mean": "11.199", - "additive": "-0.113", - "lod_score": "3.7", - "lrs_location": "Chr1: 157.588921", - "sample_r": "0.305", - "num_overlap": 67, - "sample_p": "1.200e-02", - "lit_corr": "--", - "tissue_corr": "-0.405", - "tissue_pvalue": "4.032e-02" - }, - { - "index": 8, - "trait_id": "1415742_at", - "dataset": "HC_M2_0606_P", - "hmac": "1415742_at:HC_M2_0606_P:b72a582a1f840a18c3e7", - "symbol": "Aup1", - "description": "ancient ubiquitous protein 1", - "location": "Chr6: 83.006784", - "mean": "9.529", - "additive": "-0.062", - "lod_score": "2.4", - "lrs_location": "Chr19: 16.955950", - "sample_r": "0.295", - "num_overlap": 67, - "sample_p": "1.523e-02", - "lit_corr": "--", - "tissue_corr": "-0.033", - "tissue_pvalue": "8.716e-01" - }, - { - "index": 9, - "trait_id": "1415743_at", - "dataset": "HC_M2_0606_P", - "hmac": "1415743_at:HC_M2_0606_P:3187245a079e824b4236", - "symbol": "Hdac5", - "description": "histone deacetylase 5; last four exons", - "location": "Chr11: 102.057397", - "mean": "11.009", - "additive": "0.081", - "lod_score": "2.1", - "lrs_location": "Chr7: 125.263073", - "sample_r": "0.285", - "num_overlap": 67, - "sample_p": "1.950e-02", - "lit_corr": "--", - "tissue_corr": "0.005", - "tissue_pvalue": "9.823e-01" - }, - { - "index": 10, - "trait_id": "1415690_at", - "dataset": "HC_M2_0606_P", - "hmac": "1415690_at:HC_M2_0606_P:603b215ede00b6fe1104", - "symbol": "Mrp127", - "description": "39S ribosomal protein L27, mitochondrial; last three exons", - "location": "Chr11: 94.517922", - "mean": "12.569", - "additive": "0.063", - "lod_score": "1.9", - "lrs_location": "Chr2: 164.779024", - "sample_r": "0.266", - "num_overlap": 67, - "sample_p": "2.986e-02", - "lit_corr": "--", - "tissue_corr": "--", - "tissue_pvalue": "--" - }, - { - "index": 11, - "trait_id": "1415727_at", - "dataset": "HC_M2_0606_P", - "hmac": "1415727_at:HC_M2_0606_P:cb40b8cba0eee75781a6", - "symbol": "Apoa1bp", - "description": "apolipoprotein A-I binding protein; exons 3 through 6", - "location": "Chr3: 87.860534", - "mean": "11.707", - "additive": "-0.076", - "lod_score": "2.8", - "lrs_location": "Chr3: 56.295375", - "sample_r": "0.263", - "num_overlap": 67, - "sample_p": "3.136e-02", - "lit_corr": "--", - "tissue_corr": "-0.535", - "tissue_pvalue": "4.841e-03" - }, - { - "index": 12, - "trait_id": "1415730_at", - "dataset": "HC_M2_0606_P", - "hmac": "1415730_at:HC_M2_0606_P:a970e0610a56ac4aba27", - "symbol": "Cpsf7", - "description": "cleavage and polyadenylation specificity factor 7; distal 3' UTR (transQTL on Chr 4 in BXD eye data)", - "location": "Chr19: 10.621618", - "mean": "10.662", - "additive": "-0.048", - "lod_score": "2.1", - "lrs_location": "Chr1: 188.085707", - "sample_r": "-0.263", - "num_overlap": 67, - "sample_p": "3.164e-02", - "lit_corr": "--", - "tissue_corr": "--", - "tissue_pvalue": "--" - }, - { - "index": 13, - "trait_id": "1415741_at", - "dataset": "HC_M2_0606_P", - "hmac": "1415741_at:HC_M2_0606_P:033752be361d32960c29", - "symbol": "Tmem165", - "description": "transmembrane protein 165; 3' UTR", - "location": "Chr5: 76.637708", - "mean": "10.974", - "additive": "0.048", - "lod_score": "2.0", - "lrs_location": "Chr4: 5.606394", - "sample_r": "-0.258", - "num_overlap": 67, - "sample_p": "3.489e-02", - "lit_corr": "--", - "tissue_corr": "0.271", - "tissue_pvalue": "1.812e-01" - }, - { - "index": 14, - "trait_id": "1415725_at", - "dataset": "HC_M2_0606_P", - "hmac": "1415725_at:HC_M2_0606_P:fbd6458be4f8ccbf1dc0", - "symbol": "Rrn3", - "description": "RRN3 RNA polymerase I transcription factor homolog (yeast)", - "location": "Chr16: 13.814359", - "mean": "9.195", - "additive": "-0.085", - "lod_score": "2.8", - "lrs_location": "Chr1: 148.717644", - "sample_r": "0.256", - "num_overlap": 67, - "sample_p": "3.636e-02", - "lit_corr": "--", - "tissue_corr": "0.587", - "tissue_pvalue": "1.621e-03" - }, - { - "index": 15, - "trait_id": "1415717_at", - "dataset": "HC_M2_0606_P", - "hmac": "1415717_at:HC_M2_0606_P:dd51438830e4033114f8", - "symbol": "Rnf220", - "description": "ring finger protein 220; mid 3' UTR", - "location": "Chr4: 116.944155", - "mean": "10.778", - "additive": "-0.084", - "lod_score": "2.4", - "lrs_location": "Chr4: 122.536808", - "sample_r": "0.242", - "num_overlap": 67, - "sample_p": "4.816e-02", - "lit_corr": "--", - "tissue_corr": "--", - "tissue_pvalue": "--" - }, - { - "index": 16, - "trait_id": "1415703_at", - "dataset": "HC_M2_0606_P", - "hmac": "1415703_at:HC_M2_0606_P:51ee8e47654845a546f0", - "symbol": "Huwe1", - "description": "HECT, UBA and WWE domain containing 1; last 3 exons and proximal 3' UTR", - "location": "ChrX: 148.367136", - "mean": "11.335", - "additive": "-0.094", - "lod_score": "2.3", - "lrs_location": "Chr1: 135.891043", - "sample_r": "0.235", - "num_overlap": 67, - "sample_p": "5.541e-02", - "lit_corr": "--", - "tissue_corr": "0.528", - "tissue_pvalue": "5.576e-03" - }, - { - "index": 17, - "trait_id": "1415748_a_at", - "dataset": "HC_M2_0606_P", - "hmac": "1415748_a_at:HC_M2_0606_P:749a2279081b54e89885", - "symbol": "Dctn5", - "description": "dynactin 5; last exon and proximal half of 3' UTR", - "location": "Chr7: 129.291923", - "mean": "11.250", - "additive": "0.071", - "lod_score": "3.4", - "lrs_location": "Chr5: 138.337847", - "sample_r": "0.230", - "num_overlap": 67, - "sample_p": "6.133e-02", - "lit_corr": "--", - "tissue_corr": "0.064", - "tissue_pvalue": "7.557e-01" - }, - { - "index": 18, - "trait_id": "1415706_at", - "dataset": "HC_M2_0606_P", - "hmac": "1415706_at:HC_M2_0606_P:ddfffdb78d0ff84d6a1a", - "symbol": "Copa", - "description": "coatomer protein complex, subunit alpha; 3' UTR", - "location": "Chr1: 174.051912", - "mean": "12.577", - "additive": "-0.143", - "lod_score": "8.7", - "lrs_location": "Chr1: 172.981863", - "sample_r": "0.224", - "num_overlap": 67, - "sample_p": "6.829e-02", - "lit_corr": "--", - "tissue_corr": "-0.147", - "tissue_pvalue": "4.739e-01" - }, - { - "index": 19, - "trait_id": "1415696_at", - "dataset": "HC_M2_0606_P", - "hmac": "1415696_at:HC_M2_0606_P:da00b2667d7c27dc76a2", - "symbol": "Sar1a", - "description": "SAR1 gene homolog A; distal 3' UTR", - "location": "Chr10: 61.155492", - "mean": "11.447", - "additive": "-0.051", - "lod_score": "2.4", - "lrs_location": "Chr15: 87.788313", - "sample_r": "0.220", - "num_overlap": 67, - "sample_p": "7.356e-02", - "lit_corr": "--", - "tissue_corr": "-0.559", - "tissue_pvalue": "3.015e-03" - }, - { - "index": 20, - "trait_id": "1415731_at", - "dataset": "HC_M2_0606_P", - "hmac": "1415731_at:HC_M2_0606_P:9e91e97ca1001091a5f3", - "symbol": "Angel2", - "description": "angel homolog 2; distal 3' UTR", - "location": "Chr1: 192.769800", - "mean": "9.490", - "additive": "0.062", - "lod_score": "2.6", - "lrs_location": "Chr14: 124.508018", - "sample_r": "0.218", - "num_overlap": 67, - "sample_p": "7.623e-02", - "lit_corr": "--", - "tissue_corr": "0.232", - "tissue_pvalue": "2.544e-01" - }, - { - "index": 21, - "trait_id": "1415750_at", - "dataset": "HC_M2_0606_P", - "hmac": "1415750_at:HC_M2_0606_P:c9f757736d57e5f23aa5", - "symbol": "Tbl3", - "description": "transducin (beta)-like 3", - "location": "Chr17: 24.838067", - "mean": "8.703", - "additive": "-0.132", - "lod_score": "10.0", - "lrs_location": "Chr17: 23.322636", - "sample_r": "0.213", - "num_overlap": 67, - "sample_p": "8.332e-02", - "lit_corr": "--", - "tissue_corr": "0.312", - "tissue_pvalue": "1.211e-01" - }, - { - "index": 22, - "trait_id": "1415680_at", - "dataset": "HC_M2_0606_P", - "hmac": "1415680_at:HC_M2_0606_P:22e90a54261cb373975e", - "symbol": "Anapc1", - "description": "anaphase promoting complex subunit 1; last 3 exons and 3' UTR", - "location": "Chr2: 128.438499", - "mean": "9.180", - "additive": "-0.102", - "lod_score": "8.7", - "lrs_location": "Chr2: 125.304784", - "sample_r": "-0.210", - "num_overlap": 67, - "sample_p": "8.734e-02", - "lit_corr": "--", - "tissue_corr": "0.367", - "tissue_pvalue": "6.539e-02" - }, - { - "index": 23, - "trait_id": "1415712_at", - "dataset": "HC_M2_0606_P", - "hmac": "1415712_at:HC_M2_0606_P:48e284402cb79a5fbede", - "symbol": "Zranb1", - "description": "zinc finger, RAN-binding domain containing 1 (ubiquitin thioesterase, TRAF-binding protein); far 3' UTR (M430AB control duplicate)", - "location": "Chr7: 140.175988", - "mean": "9.923", - "additive": "-0.079", - "lod_score": "2.8", - "lrs_location": "Chr5: 143.642242", - "sample_r": "-0.208", - "num_overlap": 67, - "sample_p": "9.125e-02", - "lit_corr": "--", - "tissue_corr": "-0.068", - "tissue_pvalue": "7.413e-01" - }, - { - "index": 24, - "trait_id": "1415674_a_at", - "dataset": "HC_M2_0606_P", - "hmac": "1415674_a_at:HC_M2_0606_P:c8e7fb1fcad21d73fcfd", - "symbol": "Trappc4", - "description": "trafficking protein particle complex 4; exons 3 and 4", - "location": "Chr9: 44.212489", - "mean": "10.760", - "additive": "-0.065", - "lod_score": "3.3", - "lrs_location": "Chr5: 69.527298", - "sample_r": "0.201", - "num_overlap": 67, - "sample_p": "1.028e-01", - "lit_corr": "--", - "tissue_corr": "-0.334", - "tissue_pvalue": "9.587e-02" - }, - { - "index": 25, - "trait_id": "1415747_s_at", - "dataset": "HC_M2_0606_P", - "hmac": "1415747_s_at:HC_M2_0606_P:5d86584be55f6cec47ab", - "symbol": "Riok3", - "description": "RIO kinase 3 (yeast); mid to distal 3' UTR", - "location": "Chr18: 12.314783", - "mean": "10.906", - "additive": "0.068", - "lod_score": "2.1", - "lrs_location": "Chr4: 13.764991", - "sample_r": "-0.198", - "num_overlap": 67, - "sample_p": "1.081e-01", - "lit_corr": "--", - "tissue_corr": "0.282", - "tissue_pvalue": "1.628e-01" - }, - { - "index": 26, - "trait_id": "1415682_at", - "dataset": "HC_M2_0606_P", - "hmac": "1415682_at:HC_M2_0606_P:d02febdf17a279a71088", - "symbol": "Xpo7", - "description": "exportin 7", - "location": "Chr14: 71.064730", - "mean": "9.075", - "additive": "-0.073", - "lod_score": "2.8", - "lrs_location": "Chr17: 68.421021", - "sample_r": "0.197", - "num_overlap": 67, - "sample_p": "1.092e-01", - "lit_corr": "--", - "tissue_corr": "-0.322", - "tissue_pvalue": "1.084e-01" - }, - { - "index": 27, - "trait_id": "1415732_at", - "dataset": "HC_M2_0606_P", - "hmac": "1415732_at:HC_M2_0606_P:c0010f5b42f210874883", - "symbol": "Abhd16a", - "description": "abhydrolase domain containing 16A; last five exons including proximal 3' UTR", - "location": "Chr17: 35.238940", - "mean": "10.798", - "additive": "-0.132", - "lod_score": "6.1", - "lrs_location": "Chr17: 37.015392", - "sample_r": "0.177", - "num_overlap": 67, - "sample_p": "1.527e-01", - "lit_corr": "--", - "tissue_corr": "--", - "tissue_pvalue": "--" - }, - { - "index": 28, - "trait_id": "1415688_at", - "dataset": "HC_M2_0606_P", - "hmac": "1415688_at:HC_M2_0606_P:4c3b6c7cd3d447f2346c", - "symbol": "Ube2g1", - "description": "ubiquitin-conjugating enzyme E2 G1; mid to distal 3' UTR", - "location": "Chr11: 72.497627", - "mean": "11.494", - "additive": "-0.116", - "lod_score": "7.1", - "lrs_location": "Chr11: 72.486317", - "sample_r": "-0.173", - "num_overlap": 67, - "sample_p": "1.605e-01", - "lit_corr": "--", - "tissue_corr": "0.365", - "tissue_pvalue": "6.671e-02" - }, - { - "index": 29, - "trait_id": "1415698_at", - "dataset": "HC_M2_0606_P", - "hmac": "1415698_at:HC_M2_0606_P:4d8988a8fac8bdbce9c2", - "symbol": "Golm1", - "description": "Golgi membrane protein 1; distal 3' UTR", - "location": "Chr13: 59.736417", - "mean": "11.367", - "additive": "0.113", - "lod_score": "2.9", - "lrs_location": "Chr7: 36.124856", - "sample_r": "0.151", - "num_overlap": 67, - "sample_p": "2.221e-01", - "lit_corr": "--", - "tissue_corr": "-0.053", - "tissue_pvalue": "7.958e-01" - }, - { - "index": 30, - "trait_id": "1415697_at", - "dataset": "HC_M2_0606_P", - "hmac": "1415697_at:HC_M2_0606_P:ab18358c61fbc03fdf13", - "symbol": "G3bp2", - "description": "GTPase activating protein (SH3 domain) binding protein 2; mid proximal 3' UTR", - "location": "Chr5: 92.482845", - "mean": "10.768", - "additive": "0.137", - "lod_score": "3.6", - "lrs_location": "Chr5: 138.337847", - "sample_r": "0.142", - "num_overlap": 67, - "sample_p": "2.504e-01", - "lit_corr": "--", - "tissue_corr": "0.107", - "tissue_pvalue": "6.032e-01" - }, - { - "index": 31, - "trait_id": "1415676_a_at", - "dataset": "HC_M2_0606_P", - "hmac": "1415676_a_at:HC_M2_0606_P:b236ce0b2af4408662b6", - "symbol": "Psmb5", - "description": "proteasome (prosome, macropain) subunit, beta type 5; 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