diff options
| -rw-r--r-- | src/gemma_io.cpp | 10 |
1 files changed, 10 insertions, 0 deletions
diff --git a/src/gemma_io.cpp b/src/gemma_io.cpp index 962e0c0..bd687af 100644 --- a/src/gemma_io.cpp +++ b/src/gemma_io.cpp @@ -684,6 +684,9 @@ bool ReadFile_geno(const string &file_geno, const set<string> &setSnps, double maf, geno, geno_old; size_t n_miss; size_t n_0, n_1, n_2; + double min_g = std::numeric_limits<float>::max(); + double max_g = std::numeric_limits<float>::min(); + int flag_poly; int ni_total = indicator_idv.size(); @@ -770,6 +773,8 @@ bool ReadFile_geno(const string &file_geno, const set<string> &setSnps, } gsl_vector_set(genotype, c_idv, geno); + if (geno < min_g) min_g = geno; + if (geno > max_g) max_g = geno; // going through genotypes with 0.0 < geno < 2.0 if (flag_poly == 0) { // first init in marker @@ -846,6 +851,11 @@ bool ReadFile_geno(const string &file_geno, const set<string> &setSnps, ns_test++; } + if (min_g != 0.0) + warning_msg("The minimum genotype value is not 0.0 - this is not the BIMBAM standard and will skew l_lme and effect sizes"); + if (max_g != 2.0) + warning_msg("The maximum genotype value is not 2.0 - this is not the BIMBAM standard and will skew l_lme and effect sizes"); + gsl_vector_free(genotype); gsl_vector_free(genotype_miss); gsl_matrix_free(WtW); |