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| author | Peter Carbonetto | 2017-08-07 13:23:24 -0500 |
|---|---|---|
| committer | GitHub | 2017-08-07 13:23:24 -0500 |
| commit | 7360d14216400b8f12fbfda03ac2f4827b102711 (patch) | |
| tree | 63a4031267b10f587b695adb487aca5213889b20 /src/lmm.h | |
| parent | d8db988550d4cd0303f0b82a75499c2c94d97d45 (diff) | |
| parent | 449d882a3b33ef81ef4f0127c3932b01fa796dbb (diff) | |
| download | pangemma-7360d14216400b8f12fbfda03ac2f4827b102711.tar.gz | |
Merge pull request #63 from genenetwork/loco-formatted
LOCO is implemented in GEMMA for the BIMBAM format.
Diffstat (limited to 'src/lmm.h')
| -rw-r--r-- | src/lmm.h | 6 |
1 files changed, 5 insertions, 1 deletions
diff --git a/src/lmm.h b/src/lmm.h index c393daf..4d57ab1 100644 --- a/src/lmm.h +++ b/src/lmm.h @@ -26,6 +26,8 @@ using namespace std; +#define LMM_BATCH_SIZE 10000 // used for batch processing + class FUNC_PARAM { public: @@ -78,6 +80,7 @@ public: vector<int> indicator_snp; vector<SNPINFO> snpInfo; // Record SNP information. + set<string> setGWASnps; // Record SNP information. // Not included in PARAM. vector<SUMSTAT> sumStat; // Output SNPSummary Data. @@ -97,7 +100,8 @@ public: const gsl_matrix *W, const gsl_vector *y); void AnalyzeBimbam(const gsl_matrix *U, const gsl_vector *eval, const gsl_matrix *UtW, const gsl_vector *Uty, - const gsl_matrix *W, const gsl_vector *y); + const gsl_matrix *W, const gsl_vector *y, + const set<string> gwasnps); void AnalyzePlinkGXE(const gsl_matrix *U, const gsl_vector *eval, const gsl_matrix *UtW, const gsl_vector *Uty, const gsl_matrix *W, const gsl_vector *y, |