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| author | Pjotr Prins | 2015-03-20 12:18:03 +0300 |
|---|---|---|
| committer | Pjotr Prins | 2015-03-20 12:18:03 +0300 |
| commit | 38594c7781b587a24be14b9631a73662ee3fdc2b (patch) | |
| tree | 85c363ccc3127c6245a7984f32b8c4688ec60f66 /wqflask | |
| parent | 8e9d7cde41800766fec835ca0c4a55c6327e05c8 (diff) | |
| download | genenetwork2-38594c7781b587a24be14b9631a73662ee3fdc2b.tar.gz | |
Fall back on calculate_kinship_new again
Diffstat (limited to 'wqflask')
| -rw-r--r-- | wqflask/wqflask/my_pylmm/pyLMM/lmm.py | 2 | ||||
| -rw-r--r-- | wqflask/wqflask/my_pylmm/pyLMM/runlmm.py | 2 |
2 files changed, 2 insertions, 2 deletions
diff --git a/wqflask/wqflask/my_pylmm/pyLMM/lmm.py b/wqflask/wqflask/my_pylmm/pyLMM/lmm.py index c040e3c2..a649029c 100644 --- a/wqflask/wqflask/my_pylmm/pyLMM/lmm.py +++ b/wqflask/wqflask/my_pylmm/pyLMM/lmm.py @@ -277,7 +277,7 @@ def run_other_old(pheno_vector, print("Running the original LMM engine in run_other (old)") print("REML=",restricted_max_likelihood," REFIT=",refit) with Bench("Calculate Kinship"): - kinship_matrix,genotype_matrix = calculate_kinship_old(genotype_matrix, tempdata) + kinship_matrix,genotype_matrix = calculate_kinship_new(genotype_matrix, tempdata) print("kinship_matrix: ", pf(kinship_matrix)) print("kinship_matrix.shape: ", pf(kinship_matrix.shape)) diff --git a/wqflask/wqflask/my_pylmm/pyLMM/runlmm.py b/wqflask/wqflask/my_pylmm/pyLMM/runlmm.py index 6a38da56..88e2a033 100644 --- a/wqflask/wqflask/my_pylmm/pyLMM/runlmm.py +++ b/wqflask/wqflask/my_pylmm/pyLMM/runlmm.py @@ -184,7 +184,7 @@ elif cmd == 'kinship': gnt = None if options.test_kinship: - K = kinship_full(np.copy(G)) + K = kinship_full(np.copy(G),uses) print "Genotype",G.shape, "\n", G print "first Kinship method",K.shape,"\n",K k1 = round(K[0][0],4) |