diff options
Diffstat (limited to 'src')
| -rw-r--r-- | src/io.cpp | 2 | ||||
| -rw-r--r-- | src/lmm.cpp | 137 | ||||
| -rw-r--r-- | src/lmm.h | 2 | ||||
| -rw-r--r-- | src/param.h | 2 |
4 files changed, 71 insertions, 72 deletions
diff --git a/src/io.cpp b/src/io.cpp index 71d55c3..84367ed 100644 --- a/src/io.cpp +++ b/src/io.cpp @@ -56,7 +56,7 @@ void ProgressBar(string str, double p, double total, double ratio) { cout << str << " "; cout << std::string(barsize,'='); cout << std::string(50-barsize,' '); - cout << setprecision(0) << fixed << progress << "%"; + cout << setprecision(0) << fixed << " " << progress << "%"; if (ratio != -1.0) cout << setprecision(2) << " " << ratio; cout << "\r" << flush; diff --git a/src/lmm.cpp b/src/lmm.cpp index 4bca3fb..8c90b28 100644 --- a/src/lmm.cpp +++ b/src/lmm.cpp @@ -1197,7 +1197,7 @@ void LMM::AnalyzeGene(const gsl_matrix *U, const gsl_vector *eval, for (size_t t = 0; t < ng_total; t++) { !safeGetline(infile, line).eof(); if (t % d_pace == 0 || t == ng_total - 1) { - ProgressBar("Performing Analysis ", t, ng_total - 1); + ProgressBar("Performing Analysis", t, ng_total - 1); } ch_ptr = strtok((char *)line.c_str(), " , \t"); rs = ch_ptr; @@ -1269,26 +1269,6 @@ void LMM::AnalyzeGene(const gsl_matrix *U, const gsl_vector *eval, return; } -/* - -AnalyzeBimBam, AnalyzeGene and AnalyzePlink contain duplicate logic - -and they differ now because the first has LOCO support. To add LOCO -support to PLINK we'll converge on logic and make the functions DRY. - -The functions can be split into: - -1. Initialization -2. Partially read genotype data (batch processing) -3. LMM on the submatrix -4. Collate the results -5. Cleanup - -The only thing specific regarding the input file format is (2). The -way to solve is is to put that reader in a function that gets passed -in. - - */ - void LMM::Analyze(std::function< SnpNameValues(size_t) >& fetch_snp, const gsl_matrix *U, const gsl_vector *eval, const gsl_matrix *UtW, const gsl_vector *Uty, @@ -1305,6 +1285,7 @@ void LMM::Analyze(std::function< SnpNameValues(size_t) >& fetch_snp, size_t n_index = (n_cvt + 2 + 1) * (n_cvt + 2) / 2; const size_t inds = U->size1; + enforce(inds == ni_test); gsl_vector *x = gsl_vector_alloc(inds); // #inds gsl_vector *x_miss = gsl_vector_alloc(inds); gsl_vector *Utx = gsl_vector_alloc(U->size2); @@ -1317,6 +1298,7 @@ void LMM::Analyze(std::function< SnpNameValues(size_t) >& fetch_snp, gsl_matrix *Xlarge = gsl_matrix_alloc(inds, msize); gsl_matrix *UtXlarge = gsl_matrix_alloc(inds, msize); enforce_msg(Xlarge && UtXlarge, "Xlarge memory check"); // just to be sure + enforce(Xlarge->size1 == inds); gsl_matrix_set_zero(Xlarge); gsl_matrix_set_zero(Uab); CalcUab(UtW, Uty, Uab); @@ -1375,10 +1357,12 @@ void LMM::Analyze(std::function< SnpNameValues(size_t) >& fetch_snp, } }; - for (size_t t = 0; t < indicator_snp.size(); ++t) { - // for every SNP - if (t % d_pace == 0 || t == (ns_total - 1)) { - ProgressBar("Reading SNPs ", t, ns_total - 1); + const auto num_snps = indicator_snp.size(); + const size_t progress_step = (num_snps/20>d_pace ? num_snps/20 : d_pace); + + for (size_t t = 0; t < num_snps; ++t) { + if (t % progress_step == 0 || t == (num_snps - 1)) { + ProgressBar("Reading SNPs", t, num_snps - 1); } if (indicator_snp[t] == 0) continue; @@ -1391,34 +1375,51 @@ void LMM::Analyze(std::function< SnpNameValues(size_t) >& fetch_snp, if (process_gwasnps && gwasnps.count(snp) == 0) continue; - double x_mean = 0.0; - int c_phen = 0; - int n_miss = 0; + // drop missing idv and plug mean values for missing geno + double x_total = 0.0; // sum genotype values to compute x_mean + uint pos = 0; // position in target vector + uint n_miss = 0; gsl_vector_set_zero(x_miss); for (size_t i = 0; i < ni_total; ++i) { // get the genotypes per individual and compute stats per SNP - if (indicator_idv[i] == 0) // skip individual column + if (indicator_idv[i] == 0) // skip individual continue; double geno = gs[i]; if (std::isnan(geno)) { - gsl_vector_set(x_miss, c_phen, 0.0); + gsl_vector_set(x_miss, pos, 1.0); n_miss++; } else { - gsl_vector_set(x, c_phen, geno); - gsl_vector_set(x_miss, c_phen, 1.0); - x_mean += geno; + gsl_vector_set(x, pos, geno); + x_total += geno; } - c_phen++; + pos++; } + enforce(pos == ni_test); - x_mean /= (double)(ni_test - n_miss); + const double x_mean = x_total/(double)(ni_test - n_miss); + // plug x_mean back into missing values for (size_t i = 0; i < ni_test; ++i) { - if (gsl_vector_get(x_miss, i) == 0) { + if (gsl_vector_get(x_miss, i) == 1.0) { + gsl_vector_set(x, i, x_mean); + } + } + + /* this is what below GxE does + for (size_t i = 0; i < ni_test; ++i) { + auto geno = gsl_vector_get(x, i); + if (std::isnan(geno)) { gsl_vector_set(x, i, x_mean); + geno = x_mean; + } + if (x_mean > 1.0) { + gsl_vector_set(x, i, 2 - geno); } } + */ + enforce(x->size == ni_test); + // copy genotype values for SNP into Xlarge cache gsl_vector_view Xlarge_col = gsl_matrix_column(Xlarge, c % msize); gsl_vector_memcpy(&Xlarge_col.vector, x); @@ -1513,45 +1514,43 @@ void LMM::AnalyzePlink(const gsl_matrix *U, const gsl_vector *eval, // fetch_snp is a callback function for every SNP row std::function<SnpNameValues(size_t)> fetch_snp = [&](size_t num) { - gs.assign (ni_total,nan("")); // wipe values // n_bit, and 3 is the number of magic numbers. auto t = num; infile.seekg(t * n_bit + 3); - for (size_t i = 0; i < ni_total; ++i) { - auto ci_total = 0; - auto ci_test = 0; - for (int i = 0; i < n_bit; ++i) { - infile.read(ch, 1); - bset8 = ch[0]; - - // Minor allele homozygous: 2.0; major: 0.0. - for (size_t j = 0; j < 4; ++j) { - if ((i == (n_bit - 1)) && ci_total == (int)ni_total) { - break; - } - if (indicator_idv[ci_total] == 0) { - ci_total++; - continue; - } + auto ci_total = 0; + auto ci_test = 0; + // ---- for all genotypes + for (int i = 0; i < n_bit; ++i) { + infile.read(ch, 1); + bset8 = ch[0]; - if (bset8[2 * j] == 0) { - if (bset8[2 * j + 1] == 0) { - gs[ci_test] = 2.0; - } else { - gs[ci_test] = 1.0; - } + // Minor allele homozygous: 2.0; major: 0.0. + for (size_t j = 0; j < 4; ++j) { + if ((i == (n_bit - 1)) && ci_total == (int)ni_total) { + break; + } + if (indicator_idv[ci_total] == 0) { // skip individual + ci_total++; + continue; + } + + if (bset8[2 * j] == 0) { + if (bset8[2 * j + 1] == 0) { + gs[ci_test] = 2.0; } else { - if (bset8[2 * j + 1] == 1) { - gs[ci_test] = 0.0; - } else { - gs[ci_test] = nan(""); // already set to NaN - } + gs[ci_test] = 1.0; + } + } else { + if (bset8[2 * j + 1] == 1) { + gs[ci_test] = 0.0; + } else { + gs[ci_test] = nan(""); // already set to NaN - originally was -9.0 } - - ci_total++; - ci_test++; } + + ci_total++; + ci_test++; } } string snp="unknown"; @@ -1936,7 +1935,7 @@ void LMM::AnalyzeBimbamGXE(const gsl_matrix *U, const gsl_vector *eval, for (size_t t = 0; t < indicator_snp.size(); ++t) { !safeGetline(infile, line).eof(); if (t % d_pace == 0 || t == (ns_total - 1)) { - ProgressBar("Reading SNPs ", t, ns_total - 1); + ProgressBar("Reading SNPs", t, ns_total - 1); } if (indicator_snp[t] == 0) { continue; @@ -2096,7 +2095,7 @@ void LMM::AnalyzePlinkGXE(const gsl_matrix *U, const gsl_vector *eval, for (vector<SNPINFO>::size_type t = 0; t < snpInfo.size(); ++t) { if (t % d_pace == 0 || t == snpInfo.size() - 1) { - ProgressBar("Reading SNPs ", t, snpInfo.size() - 1); + ProgressBar("Reading SNPs", t, snpInfo.size() - 1); } if (indicator_snp[t] == 0) { continue; diff --git a/src/lmm.h b/src/lmm.h index 44564f5..c02325d 100644 --- a/src/lmm.h +++ b/src/lmm.h @@ -28,7 +28,7 @@ using namespace std; -#define LMM_BATCH_SIZE 10000 // used for batch processing +#define LMM_BATCH_SIZE 1000 // used for batch processing class FUNC_PARAM { diff --git a/src/param.h b/src/param.h index 4b473c0..efea99a 100644 --- a/src/param.h +++ b/src/param.h @@ -26,7 +26,7 @@ #include <set> #include <vector> -#define K_BATCH_SIZE 10000 // #snps used for batched K +#define K_BATCH_SIZE 1000 // #snps used for batched K #define DEFAULT_PACE 1000 using namespace std; |