aboutsummaryrefslogtreecommitdiff
path: root/src/param.cpp
diff options
context:
space:
mode:
Diffstat (limited to 'src/param.cpp')
-rw-r--r--src/param.cpp84
1 files changed, 75 insertions, 9 deletions
diff --git a/src/param.cpp b/src/param.cpp
index 0a63a16..4b8c3a4 100644
--- a/src/param.cpp
+++ b/src/param.cpp
@@ -57,6 +57,7 @@ pheno_mean(0), noconstrain (false),
h_min(-1), h_max(-1), h_scale(-1),
rho_min(0.0), rho_max(1.0), rho_scale(-1),
logp_min(0.0), logp_max(0.0), logp_scale(-1),
+h_ngrid(10), rho_ngrid(10),
s_min(0), s_max(300),
w_step(100000), s_step(1000000),
r_pace(10), w_pace(1000),
@@ -66,7 +67,7 @@ geo_mean(2000.0),
randseed(-1),
window_cm(0), window_bp(0), window_ns(0), n_block(200),
error(false),
-ni_subsample(0), n_cvt(1), n_vc(1),
+ni_subsample(0), n_cvt(1), n_vc(1), n_cat(0),
time_total(0.0), time_G(0.0), time_eigen(0.0), time_UtX(0.0), time_UtZ(0.0), time_opt(0.0), time_Omega(0.0)
{}
@@ -76,7 +77,14 @@ time_total(0.0), time_G(0.0), time_eigen(0.0), time_UtX(0.0), time_UtZ(0.0), tim
void PARAM::ReadFiles (void)
{
string file_str;
-
+ /*
+ //read continuous cat file
+ if (!file_mcatc.empty()) {
+ if (ReadFile_mcatc (file_mcatc, mapRS2catc, n_cat)==false) {error=true;}
+ } else if (!file_catc.empty()) {
+ if (ReadFile_catc (file_catc, mapRS2catc, n_cat)==false) {error=true;}
+ }
+ */
//read cat file
if (!file_mcat.empty()) {
if (ReadFile_mcat (file_mcat, mapRS2cat, n_vc)==false) {error=true;}
@@ -398,7 +406,7 @@ void PARAM::CheckParam (void)
//check parameters
if (k_mode!=1 && k_mode!=2) {cout<<"error! unknown kinship/relatedness input mode: "<<k_mode<<endl; error=true;}
- if (a_mode!=1 && a_mode!=2 && a_mode!=3 && a_mode!=4 && a_mode!=5 && a_mode!=11 && a_mode!=12 && a_mode!=13 && a_mode!=14 && a_mode!=21 && a_mode!=22 && a_mode!=25 && a_mode!=26 && a_mode!=27 && a_mode!=28 && a_mode!=31 && a_mode!=41 && a_mode!=42 && a_mode!=43 && a_mode!=51 && a_mode!=52 && a_mode!=53 && a_mode!=54 && a_mode!=61 && a_mode!=62 && a_mode!=66 && a_mode!=67 && a_mode!=71)
+ if (a_mode!=1 && a_mode!=2 && a_mode!=3 && a_mode!=4 && a_mode!=5 && a_mode!=11 && a_mode!=12 && a_mode!=13 && a_mode!=14 && a_mode!=15 && a_mode!=21 && a_mode!=22 && a_mode!=25 && a_mode!=26 && a_mode!=27 && a_mode!=28 && a_mode!=31 && a_mode!=41 && a_mode!=42 && a_mode!=43 && a_mode!=51 && a_mode!=52 && a_mode!=53 && a_mode!=54 && a_mode!=61 && a_mode!=62 && a_mode!=63 && a_mode!=66 && a_mode!=67 && a_mode!=71)
{cout<<"error! unknown analysis mode: "<<a_mode<<". make sure -gk or -eigen or -lmm or -bslmm -predict or -calccov is sepcified correctly."<<endl; error=true;}
if (miss_level>1) {cout<<"error! missing level needs to be between 0 and 1. current value = "<<miss_level<<endl; error=true;}
if (maf_level>0.5) {cout<<"error! maf level needs to be between 0 and 0.5. current value = "<<maf_level<<endl; error=true;}
@@ -550,7 +558,7 @@ void PARAM::CheckParam (void)
// WJA added
if (!file_oxford.empty()) {flag++;}
- if (flag!=1 && a_mode!=27 && a_mode!=28 && a_mode!=43 && a_mode!=5 && a_mode!=61 && a_mode!=62 && a_mode!=66 && a_mode!=67) {
+ if (flag!=1 && a_mode!=15 && a_mode!=27 && a_mode!=28 && a_mode!=43 && a_mode!=5 && a_mode!=61 && a_mode!=62 && a_mode!=63 && a_mode!=66 && a_mode!=67) {
cout<<"error! either plink binary files, or bimbam mean genotype files, or gene expression files are required."<<endl; error=true;
}
@@ -578,6 +586,16 @@ void PARAM::CheckParam (void)
}
}
+
+ if (a_mode==63) {
+ if (file_kin.empty() && (file_ku.empty()||file_kd.empty()) && file_mk.empty() ) {
+ cout<<"error! missing relatedness file. "<<endl; error=true;
+ }
+ if ( file_pheno.empty() ) {
+ cout<<"error! missing phenotype file."<<endl; error=true;
+ }
+ }
+
if (a_mode==66 || a_mode==67) {
if (file_beta.empty() || ( file_mbfile.empty() && file_bfile.empty() && file_mgeno.empty() && file_geno.empty()) ) {
cout<<"error! missing beta file or genotype file."<<endl; error=true;
@@ -630,7 +648,7 @@ void PARAM::CheckParam (void)
if ((a_mode==43) && file_kin.empty()) {cout<<"error! missing relatedness file. -predict option requires -k option to provide a relatedness file."<<endl; error=true;}
- if ((a_mode==11 || a_mode==12 || a_mode==13) && !file_cvt.empty() ) {cout<<"error! -bslmm option does not support covariates files."<<endl; error=true;}
+ if ((a_mode==11 || a_mode==12 || a_mode==13 || a_mode==14 || a_mode==16) && !file_cvt.empty() ) {cout<<"error! -bslmm option does not support covariates files."<<endl; error=true;}
if (a_mode==41 || a_mode==42) {
if (!file_cvt.empty() ) {cout<<"error! -predict option does not support covariates files."<<endl; error=true;}
@@ -738,7 +756,7 @@ void PARAM::CheckData (void) {
}
}
*/
- if (ni_test==0 && file_cor.empty() && file_mstudy.empty() && file_study.empty() && file_beta.empty() ) {
+ if (ni_test==0 && file_cor.empty() && file_mstudy.empty() && file_study.empty() && file_beta.empty() && file_bf.empty() ) {
error=true;
cout<<"error! number of analyzed individuals equals 0. "<<endl;
return;
@@ -759,7 +777,7 @@ void PARAM::CheckData (void) {
}
//output some information
- if (file_cor.empty() && file_mstudy.empty() && file_study.empty() && a_mode!=27 && a_mode!=28) {
+ if (file_cor.empty() && file_mstudy.empty() && file_study.empty() && a_mode!=15 && a_mode!=27 && a_mode!=28) {
cout<<"## number of total individuals = "<<ni_total<<endl;
if (a_mode==43) {
cout<<"## number of analyzed individuals = "<<ni_cvt<<endl;
@@ -806,7 +824,7 @@ void PARAM::CheckData (void) {
//set parameters for BSLMM
//and check for predict
- if (a_mode==11 || a_mode==12 || a_mode==13) {
+ if (a_mode==11 || a_mode==12 || a_mode==13 || a_mode==14) {
if (a_mode==11) {n_mh=1;}
if (logp_min==0) {logp_min=-1.0*log((double)ns_test);}
@@ -1598,7 +1616,7 @@ void PARAM::ProcessCvtPhen ()
}
//check ni_test
- if (ni_test==0) {
+ if (ni_test==0 && a_mode!=15) {
error=true;
cout<<"error! number of analyzed individuals equals 0. "<<endl;
return;
@@ -1641,6 +1659,54 @@ void PARAM::CopyCvt (gsl_matrix *W)
return;
}
+/*
+//if there is a column contains all 1's, then flag==1; otherwise flag=0
+void PARAM::CopyA (size_t flag, gsl_matrix *A)
+{
+ size_t ci_test=0;
+ string rs;
+ vector<size_t> flag_vec;
+ vector<double> catc;
+
+ for (size_t j=0; j<n_cat; j++) {
+ flag_vec.push_back(0);
+ }
+
+ for (vector<int>::size_type i=0; i<indicator_snp.size(); ++i) {
+ if (indicator_snp[i]==0) {continue;}
+ rs=snpInfo[i].rs_number;
+
+ if (mapRS2catc.count(rs)==0) {
+ for (size_t j=0; j<n_cat; j++) {
+ gsl_matrix_set (A, ci_test, j, 0);
+ }
+ } else {
+ for (size_t j=0; j<n_cat; j++) {
+ gsl_matrix_set (A, ci_test, j, mapRS2catc[rs][j]);
+ }
+ }
+
+ if (ci_test==0) {
+ for (size_t j=0; j<n_cat; j++) {
+ catc.push_back(mapRS2catc[rs][j]);
+ }
+ } else {
+ for (size_t j=0; j<n_cat; j++) {
+ if (catc[j]==mapRS2catc[rs][j]) {flag_vec[j]++;};
+ }
+ }
+
+ ci_test++;
+ }
+
+ flag=0;
+ for (size_t j=0; j<n_cat; j++) {
+ if (flag_vec[j]==0) {flag++;}
+ }
+
+ return;
+}
+*/
void PARAM::CopyGxe (gsl_vector *env)
{
generated by cgit v1.2.3 (git 2.44.0) at 2025-01-18 19:23:16 +0000