[Genabel-commits] r625 - in pkg/VariABEL: . R src
noreply at r-forge.r-project.org
noreply at r-forge.r-project.org
Fri Dec 17 10:25:45 CET 2010
Author: maksim
Date: 2010-12-17 10:25:45 +0100 (Fri, 17 Dec 2010)
New Revision: 625
Modified:
pkg/VariABEL/DESCRIPTION
pkg/VariABEL/NAMESPACE
pkg/VariABEL/R/var.test.gwaa.R
pkg/VariABEL/src/gtps_container.cpp
pkg/VariABEL/src/supplementary_functions.cpp
pkg/VariABEL/src/supplementary_functions.h
pkg/VariABEL/src/tags
pkg/VariABEL/src/var_homogeneity_test_C.cpp
pkg/VariABEL/src/var_homogeneity_tests.cpp
pkg/VariABEL/src/var_homogeneity_tests.h
Log:
The linear regression on a squared trait with prior mean centralization is included. Itearatot is used for data obtaining.
Modified: pkg/VariABEL/DESCRIPTION
===================================================================
--- pkg/VariABEL/DESCRIPTION 2010-12-16 23:06:08 UTC (rev 624)
+++ pkg/VariABEL/DESCRIPTION 2010-12-17 09:25:45 UTC (rev 625)
@@ -1,13 +1,12 @@
-Package: VarABEL
+Package: VariABEL
Type: Package
-Title: genome-wide SNP association analysis
-Version: 1.5-0
+Title: Testing of genotypic variance heterogeneity to detect potentially interacting SNP.
+Version: 0.0-1
Date: 2010-02-18
-Author: Yurii Aulchenko, Maksim Struchalin
-Maintainer: Yurii Aulchenko <i.aoultchenko at erasmusmc.nl>
-Depends: R (>= 2.4.0), methods, MASS
-Suggests: qvalue, genetics, haplo.stats, DatABEL
-Description: a package for genome-wide association analysis between
- quantitative or binary traits and single-nucleiotide
- polymorphisms (SNPs).
+Author: Maksim Struchalin
+Maintainer: Maksim Struchalin <m.struchalin at erasmusmc.nl>
+Depends:
+Suggests:
+Description: Presence of interaction between a SNP and another SNP (or another factor) can result into heterogeneity of variance for a SNP involved into
+ interaction. Detecting of such heterogeneity for a given can give prior knowlidge for constructing a genetic model underlying complex trait.
License: GPL (>= 2)
Modified: pkg/VariABEL/NAMESPACE
===================================================================
--- pkg/VariABEL/NAMESPACE 2010-12-16 23:06:08 UTC (rev 624)
+++ pkg/VariABEL/NAMESPACE 2010-12-17 09:25:45 UTC (rev 625)
@@ -1,8 +1,9 @@
-useDynLib(VarABEL)
+useDynLib(VariABEL)
export(
var.meta.gwaa,
- var.test.gwaa
+ var.test.gwaa,
+ test_databel
)
Modified: pkg/VariABEL/R/var.test.gwaa.R
===================================================================
--- pkg/VariABEL/R/var.test.gwaa.R 2010-12-16 23:06:08 UTC (rev 624)
+++ pkg/VariABEL/R/var.test.gwaa.R 2010-12-17 09:25:45 UTC (rev 625)
@@ -24,90 +24,120 @@
#_____________________________________________________________________________________________________________________________
#Available for user function for genome-wide testing variance homogeneity of trait's distribution.
#
-"var.test.gwaa" <- function(genotype, trait, testname, analysis_type)
+"var.test.gwaa" <- function(formula, genodata, phenodata, testname="sqlm", analysis_type="AAvsABvsBB")
{
-#test statistics for each SNP is stored here. There is column names: "snpname", "chisq_df2", "chisq_df1"
-results <- data.frame()
+if(testname == "bartlett") {testname <- 0}
+else if(testname == "levene") {testname <- 1}
+else if(testname == "likelihood") {testname <- 2}
+else if(testname == "kolmogorov_smirnov") {testname <- 3}
+else if(testname == "sqlm") {testname <- 4}
+else {stop(paste(testname, "is unsupportive type of test. Only levene, and sqlm are supported."))}
-
-# Check wether the class and value of input parameters is appropriate
-#_____________________________________________________________
-if(!is(genotype, "snp.data") & !is(genotype, "numeric"))
+
+if(analysis_type == "AAvsABvsBB") {analysis_type <- 0}
+else if(analysis_type == "AAvsABandBB") {analysis_type <- 1}
+else if(analysis_type == "ABvsAAandBB") {analysis_type <- 2}
+else if(analysis_type == "BBvsAAandAB") {analysis_type <- 3}
+else {stop(paste(analysis_type, "is unsupportive type of analysis. Only AAvsABvsBB, AAvsABandBB, ABvsAAandBB, and BBvsAAandAB are supported."))}
+
+
+MAR <- 2
+OUT <- "R"
+FUN <- "variance_homogeneity_test_C_wrapper"
+
+design_matrix <- model.matrix(formula, data = phenodata)
+trat_name <- as.character(formula[[2]])
+trait <- phenodata[,trat_name]
+idnum <- length(trait)
+design_matrix_df <- data.frame(design_matrix)
+design_matrix_df$snp <- 0 #will be filled into iterator
+
+
+p <- dim(design_matrix_df)[2] #covariates number + 1
+
+print(design_matrix_df)
+gtNrow <- NA
+gtNcol <- NA
+
+#Stolen from MixABEL:
+if(class(genodata) == "snp.data")
{
- stop("VarABEL, var.test.gwaa: Wrong class of input parameter \"genotype\".")
+ gtNrow <- dim(genodata)[1]
+ gtNcol <- dim(genodata)[2]
+ genodata <- as.raw(genodata at gtps)
}
-
-if(!is(trait, "numeric"))
+ else if (class(genodata) == "matrix")
{
- stop("VarABEL, var.test.gwaa: Wrong class of input parameter \"trait\".")
+ gtNrow <- dim(genodata)[1]
+ gtNcol <- dim(genodata)[2]
+ storage.mode(genodata) <- "double"
}
-
-if(!is(testname, "character"))
+ else if (class(genodata)=="databel")
{
- stop("VarABEL, var.test.gwaa: Wrong class of input parameter \"testname\". It should be \"character\".")
+ gtNrow <- dim(genodata)[1]
+ gtNcol <- dim(genodata)[2]
+ genodata <- genodata at data
}
+ else
+ {
+ stop(paste("genodata class not recognised ('",class(genodata),"')",sep=""))
+ }
+
-#_____________________________________________________________
+results_C <- .Call("iterator", genodata,
+ as.integer(gtNrow), as.integer(gtNcol),
+ as.character(FUN),
+ as.character(OUT),
+ as.integer(MAR),
+ as.integer(1),
+ as.integer(17), #iterator additional inputa parameters number
+ as.double(trait),
+ as.double(data.matrix(design_matrix_df)),
+ as.integer(p),
+ as.integer(analysis_type),
+ as.integer(testname),
+ double(p),#betas
+ double(p),#se
+ double(1),#chi2
+ integer(1),#df
+ double(idnum),#residuals
+ double(idnum),#qty
+ integer(p),#jpvt
+ double(p),#qraux
+ double(2*p),#work
+ double(p*p),#v
+ double(p*p),#x_for_ch2inv
+ integer(idnum)
+ )
+if(class(genodata) == "snp.data")
+ {
+
+ }
-return_val <- .Call("variance_homogeneity_test_C_old_data_type",
- as.raw(genotype at gtps),
- as.double(trait),
- as.integer(genotype at nids),
- as.integer(genotype at nsnps),
- analysis_type,
- testname)
+results_df <- data.frame(results_C)
+cov_names <- colnames(design_matrix_df)
+print("1")
+output_column_names <- c("chisq", "df", "Intercept_effect", "Intercept_sd")
+print("2")
+for(i in 2:p)
+ {
+ output_column_names <- c(output_column_names, paste(cov_names[i], "_effect", sep=""))
+ output_column_names <- c(output_column_names, paste(cov_names[i], "_sd", sep=""))
+ }
+colnames(results_df) <- output_column_names
-result_df <- data.frame(chisq=return_val[[1]], df=return_val[[2]])
-
-
-#output <- .Call("interaction_rare_recesive_allele_C_", as.raw(data at gtps), as.integer(data at nids), as.integer(snp_number),
-# as.integer(trait),
-# as.integer(window),
-# return_all_result,
-# test,
-# as.integer(min_expected_cut_off))
-
-
+print(results_df)
}
-##Perform variance analysis
-##_____________________________________________________________
-#
-#if(is(genotype, "snp.data"))
-# {
-# nids <- genotype at nid
-# nsnps <- genotype at gtdata@nsnps
-# MAR <- 1
-# OUT <- "R"
-#
-# FUN <- test_C_function_name[testname] #choose name of variance homogeneity test
-#
-# #Run choosen variance homogeneity test
-# results_C <- .Call("iterator", as.raw(genotype at gtps),
-# as.integer(nids), as.integer(nsnps),
-# as.character(FUN),
-# as.character(OUT),
-# as.integer(MAR),
-# as.integer(0),
-# package="VarABEL")
-# }
-#
-#
-#
-#return results
-#}
-##End of var.test.gwaa function
-##_____________________________________________________________________________________________________________________________
-
Modified: pkg/VariABEL/src/gtps_container.cpp
===================================================================
--- pkg/VariABEL/src/gtps_container.cpp 2010-12-16 23:06:08 UTC (rev 624)
+++ pkg/VariABEL/src/gtps_container.cpp 2010-12-17 09:25:45 UTC (rev 625)
@@ -105,7 +105,7 @@
{
get_our_byte_number_and_local_person_number(id_position, snp_position); //calculate our_byte_number value
-char our_byte_vallue = gtps_array[our_byte_number-1];
+//char our_byte_vallue = gtps_array[our_byte_number-1];
@@ -129,7 +129,7 @@
std::cout<<"gtps_array[0]="<<int(gtps_array[0])<<"\n";
-for(int i=0 ; i<nbytes_for_one_snp; i++)
+for(unsigned int i=0 ; i<nbytes_for_one_snp; i++)
{
gtps_for_one_snp[i]=gtps_array[our_byte_number-1+i];
}
@@ -151,6 +151,7 @@
{
if(do_we_have_strand_and_codding_arrays) return strand_array[snp_position-1];
else std::cout<<"gtps_container::get_strand: You can not get strand since you create object with constructor gtps_container(char * gtps_array_raw, unsigned id_numbers, unsigned snp_numbers)\n";
+return char(0);
}
@@ -159,6 +160,7 @@
{
if(do_we_have_strand_and_codding_arrays) return coding_array[snp_position-1];
else std::cout<<"gtps_container::get_strand: You can not get strand since you create object with constructor gtps_container(char * gtps_array_raw, unsigned id_numbers, unsigned snp_numbers)\n";
+return char(0);
}
Modified: pkg/VariABEL/src/supplementary_functions.cpp
===================================================================
--- pkg/VariABEL/src/supplementary_functions.cpp 2010-12-16 23:06:08 UTC (rev 624)
+++ pkg/VariABEL/src/supplementary_functions.cpp 2010-12-17 09:25:45 UTC (rev 625)
@@ -195,7 +195,7 @@
Snp_store_type::iterator iter_map = snps_storage->find(snp->snpname);
-char delim=' ';
+//char delim=' ';
@@ -862,10 +862,9 @@
-
//The function break_trait_up_into_groups takes phenotype and snp, break the phenotype up on three genotypic groups.
//_________________________________________________________________________________________________
-void break_trait_up_into_groups(std::list<my_small_vector> *trait_groups, int* snp, double *trait, unsigned* nids, analysis_type_enum analys_type, int * is_trait_na)
+void break_trait_up_into_groups(std::list<my_small_vector> *trait_groups, double* snp, double *trait, long unsigned* nids, int analys_type, int * is_trait_na)
{
std::vector<double> NA, AA, AB, BB; // here we will store trait for different genotype group
@@ -875,8 +874,16 @@
//std::cout<<"break_trait_up_into_groups: trait["<<id<<"]="<<trait[id]<<", is_trait_na["<<id<<"]="<<is_trait_na[id]<<", snp["<<id<<"]="<<snp[id]<<"\n";
if(is_trait_na[id] == 1) continue;
+ //get bestguess:
+ //________________
+ static int snp_value;
+ if(snp[id]>=0. && snp[id]<0.5 ) snp_value=0;
+ if(snp[id]>=0.5 && snp[id]<=1.5 ) snp_value=1;
+ if(snp[id]>1.5 && snp[id]<=2. ) snp_value=2;
+ //________________
+
//spread ids trait among genotype group
- switch(snp[id])
+ switch(snp_value)
{
case 0:
{
@@ -937,12 +944,12 @@
//_________________________________________________
- unsigned NA_size = NA.size();
+// unsigned NA_size = NA.size();
unsigned AA_size = AA.size();
unsigned AB_size = AB.size();
unsigned BB_size = BB.size();
- double *na, *aa, *ab, *bb;
+ double /**na,*/ *aa, *ab, *bb;
if(AA_size > 1)
@@ -997,7 +1004,6 @@
-
//________________________________________________________
// For qsort function
int compare_doubles(const void *a, const void *b)
Modified: pkg/VariABEL/src/supplementary_functions.h
===================================================================
--- pkg/VariABEL/src/supplementary_functions.h 2010-12-16 23:06:08 UTC (rev 624)
+++ pkg/VariABEL/src/supplementary_functions.h 2010-12-17 09:25:45 UTC (rev 625)
@@ -97,7 +97,7 @@
}
double * vector;
- unsigned long number; //amount of cells in vector
+ long number; //amount of cells in vector
};
@@ -138,9 +138,6 @@
-enum analysis_type_enum {AAvsABvsBB, AAvsABandBB, ABvsAAandBB, BBvsAAandAB};
-enum testname_enum {bartlett, levene, likelihood, kolmogorov_smirnov};
-
bool include_snp(Snp_store_type *, snp_var_data*, std::ofstream & warnings_file, char *testname); //include snp into common storage
snp_var_data* snp_var_meta(snp_var_data* , snp_var_data*, char* testname); //metaanalysis of two snps
bool is_na(const VARIABLE_TYPE val, const VARIABLE_TYPE na_reference=NA_value); //is numerical value recognized as NA
@@ -161,6 +158,21 @@
bool snp_filter(snp_var_data* snp, std::ofstream & warnings_file, bool exclude_whole_snp, unsigned threshold, bool do_warnings_output);
bool check_files_format(const char** filenames, unsigned file_amount, unsigned skip_first_lines_amount, char delim);
-void break_trait_up_into_groups(std::list<my_small_vector> *trait_groups, int* snp, double *trait, unsigned* nids, analysis_type_enum analys_type_, int * is_trait_na);
+void break_trait_up_into_groups(std::list<my_small_vector> *trait_groups, double* snp, double *trait, long unsigned* nids, int analys_type, int * is_trait_na);
+
+const short unsigned int AAvsABvsBB = 0;
+const short unsigned int AAvsABandBB = 1;
+const short unsigned int ABvsAAandBB = 2;
+const short unsigned int BBvsAAandAB = 3;
+
+const short unsigned int bartlett = 0;
+const short unsigned int levene = 1;
+const short unsigned int likelihood = 2;
+const short unsigned int kolmogorov_smirnov = 3;
+const short unsigned int sqlm=4;
+
+
+
+
#endif
Modified: pkg/VariABEL/src/tags
===================================================================
--- pkg/VariABEL/src/tags 2010-12-16 23:06:08 UTC (rev 624)
+++ pkg/VariABEL/src/tags 2010-12-17 09:25:45 UTC (rev 625)
@@ -4,105 +4,899 @@
!_TAG_PROGRAM_NAME Exuberant Ctags //
!_TAG_PROGRAM_URL http://ctags.sourceforge.net /official site/
!_TAG_PROGRAM_VERSION 5.6 //
+AAvsABandBB VARlib/supplementary_functions.h /^enum analysis_type_enum {AAvsABvsBB, AAvsABandBB, ABvsAAandBB, BBvsAAandAB};$/;" e enum:analysis_type_enum
AAvsABandBB supplementary_functions.h /^enum analysis_type_enum {AAvsABvsBB, AAvsABandBB, ABvsAAandBB, BBvsAAandAB};$/;" e enum:analysis_type_enum
+AAvsABvsBB VARlib/supplementary_functions.h /^enum analysis_type_enum {AAvsABvsBB, AAvsABandBB, ABvsAAandBB, BBvsAAandAB};$/;" e enum:analysis_type_enum
AAvsABvsBB supplementary_functions.h /^enum analysis_type_enum {AAvsABvsBB, AAvsABandBB, ABvsAAandBB, BBvsAAandAB};$/;" e enum:analysis_type_enum
+ABvsAAandBB VARlib/supplementary_functions.h /^enum analysis_type_enum {AAvsABvsBB, AAvsABandBB, ABvsAAandBB, BBvsAAandAB};$/;" e enum:analysis_type_enum
ABvsAAandBB supplementary_functions.h /^enum analysis_type_enum {AAvsABvsBB, AAvsABandBB, ABvsAAandBB, BBvsAAandAB};$/;" e enum:analysis_type_enum
+AbstractMatrix AbstractMatrix.h /^class AbstractMatrix {$/;" c
+AbstractMatrix fvlib/AbstractMatrix.h /^class AbstractMatrix {$/;" c
+AbstractMatrixRFinalizer AbstractMatrix_R.cpp /^ static void AbstractMatrixRFinalizer(SEXP x) {$/;" f file:
+AbstractMatrixRFinalizer DAlib/AbstractMatrix_R.cpp /^ static void AbstractMatrixRFinalizer(SEXP x) {$/;" f file:
+BBvsAAandAB VARlib/supplementary_functions.h /^enum analysis_type_enum {AAvsABvsBB, AAvsABandBB, ABvsAAandBB, BBvsAAandAB};$/;" e enum:analysis_type_enum
BBvsAAandAB supplementary_functions.h /^enum analysis_type_enum {AAvsABvsBB, AAvsABandBB, ABvsAAandBB, BBvsAAandAB};$/;" e enum:analysis_type_enum
+CHAR_NAN CastUtils.cpp /^char CHAR_NAN;$/;" v
+CHAR_NAN fvlib/CastUtils.cpp /^char CHAR_NAN;$/;" v
+COPY_AND_COMPARE CastUtils.h 38;" d
+COPY_AND_COMPARE fvlib/CastUtils.h 38;" d
+COUNTS VARlib/supplementary_functions.h /^ int COUNTS[GENO_TYPES_NUM];$/;" m struct:snp_var_data
COUNTS supplementary_functions.h /^ int COUNTS[GENO_TYPES_NUM];$/;" m struct:snp_var_data
+CPP_dqrls AbstractMatrix_R.cpp /^ void CPP_dqrls($/;" f
+CPP_dqrls DAlib/AbstractMatrix_R.cpp /^ void CPP_dqrls($/;" f
+DB_CREATE FileVector.h 26;" d
+DB_CREATE fvlib/FileVector.h 26;" d
+DB_EXCL FileVector.h 27;" d
+DB_EXCL fvlib/FileVector.h 27;" d
+DB_RDONLY FileVector.h 28;" d
+DB_RDONLY fvlib/FileVector.h 28;" d
+DEBUG_LEVEL Logger.h 17;" d
+DEBUG_LEVEL fvlib/Logger.h 17;" d
+DOUBLE const.h 13;" d
+DOUBLE fvlib/const.h 13;" d
+ERROR_LEVEL Logger.h 18;" d
+ERROR_LEVEL fvlib/Logger.h 18;" d
+ErrorExit Logger.h /^class ErrorExit {};$/;" c
+ErrorExit fvlib/Logger.h /^class ErrorExit {};$/;" c
+FILEVECTOR_DATA_FILE_SUFFIX FileVector.h /^const string FILEVECTOR_DATA_FILE_SUFFIX = ".fvd";$/;" v
+FILEVECTOR_DATA_FILE_SUFFIX fvlib/FileVector.h /^const string FILEVECTOR_DATA_FILE_SUFFIX = ".fvd";$/;" v
+FILEVECTOR_INDEX_FILE_SUFFIX FileVector.h /^const string FILEVECTOR_INDEX_FILE_SUFFIX = ".fvi";$/;" v
+FILEVECTOR_INDEX_FILE_SUFFIX fvlib/FileVector.h /^const string FILEVECTOR_INDEX_FILE_SUFFIX = ".fvi";$/;" v
+FLOAT const.h 12;" d
+FLOAT fvlib/const.h 12;" d
+FV_AUTHORS frversion.h 6;" d
+FV_AUTHORS fvlib/frversion.h 6;" d
+FV_RELEASEDATE frversion.h 5;" d
+FV_RELEASEDATE fvlib/frversion.h 5;" d
+FV_VERSION frversion.h 4;" d
+FV_VERSION fvlib/frversion.h 4;" d
+FileHeader frutil.h /^ FileHeader () {$/;" f class:FileHeader
+FileHeader frutil.h /^class FileHeader$/;" c
+FileHeader fvlib/frutil.h /^ FileHeader () {$/;" f class:FileHeader
+FileHeader fvlib/frutil.h /^class FileHeader$/;" c
+FileVector FileVector.h /^ FileVector(char *iFilename, unsigned long cachesizeMb) : filename(string(iFilename)){$/;" f class:FileVector
+FileVector FileVector.h /^ FileVector(char *iFilename, unsigned long cachesizeMb, bool iReadOnly) : filename(string(iFilename)), readOnly(iReadOnly) {$/;" f class:FileVector
+FileVector FileVector.h /^ FileVector(string iFilename, unsigned long cachesizeMb) : filename (iFilename) {$/;" f class:FileVector
+FileVector FileVector.h /^ FileVector(string iFilename, unsigned long cachesizeMb, bool iReadOnly) : filename(iFilename), readOnly(iReadOnly) {$/;" f class:FileVector
+FileVector FileVector.h /^class FileVector: public AbstractMatrix {$/;" c
+FileVector fvlib/FileVector.h /^ FileVector(char *iFilename, unsigned long cachesizeMb) : filename(string(iFilename)){$/;" f class:FileVector
+FileVector fvlib/FileVector.h /^ FileVector(char *iFilename, unsigned long cachesizeMb, bool iReadOnly) : filename(string(iFilename)), readOnly(iReadOnly) {$/;" f class:FileVector
+FileVector fvlib/FileVector.h /^ FileVector(string iFilename, unsigned long cachesizeMb) : filename (iFilename) {$/;" f class:FileVector
+FileVector fvlib/FileVector.h /^ FileVector(string iFilename, unsigned long cachesizeMb, bool iReadOnly) : filename(iFilename), readOnly(iReadOnly) {$/;" f class:FileVector
+FileVector fvlib/FileVector.h /^class FileVector: public AbstractMatrix {$/;" c
+FilteredAndAbstractRFinalizer DAlib/FilteredMatrix_R.cpp /^ static void FilteredAndAbstractRFinalizer(SEXP x) {$/;" f file:
+FilteredAndAbstractRFinalizer FilteredMatrix_R.cpp /^ static void FilteredAndAbstractRFinalizer(SEXP x) {$/;" f file:
+FilteredMatrix FilteredMatrix.h /^ FilteredMatrix(AbstractMatrix &matrix) : nestedMatrix(&matrix) {$/;" f class:FilteredMatrix
+FilteredMatrix FilteredMatrix.h /^class FilteredMatrix : public AbstractMatrix {$/;" c
+FilteredMatrix fvlib/FilteredMatrix.h /^ FilteredMatrix(AbstractMatrix &matrix) : nestedMatrix(&matrix) {$/;" f class:FilteredMatrix
+FilteredMatrix fvlib/FilteredMatrix.h /^class FilteredMatrix : public AbstractMatrix {$/;" c
+FilteredMatrixRFinalizer DAlib/FilteredMatrix_R.cpp /^ static void FilteredMatrixRFinalizer(SEXP x) {$/;" f file:
+FilteredMatrixRFinalizer FilteredMatrix_R.cpp /^ static void FilteredMatrixRFinalizer(SEXP x) {$/;" f file:
+FixedChar frutil.h /^ FixedChar(){$/;" f class:FixedChar
+FixedChar frutil.h /^ FixedChar(string s){$/;" f class:FixedChar
+FixedChar frutil.h /^class FixedChar$/;" c
+FixedChar fvlib/frutil.h /^ FixedChar(){$/;" f class:FixedChar
+FixedChar fvlib/frutil.h /^ FixedChar(string s){$/;" f class:FixedChar
+FixedChar fvlib/frutil.h /^class FixedChar$/;" c
+GENO VARlib/supplementary_functions.h /^ std::string GENO[GENO_TYPES_NUM];$/;" m struct:snp_var_data
GENO supplementary_functions.h /^ std::string GENO[GENO_TYPES_NUM];$/;" m struct:snp_var_data
+GENO_TYPES_NUM VARlib/supplementary_functions.h 39;" d
+GENO_TYPES_NUM VARlib/var_meta_gwaa_C.cpp 79;" d file:
GENO_TYPES_NUM supplementary_functions.h 39;" d
GENO_TYPES_NUM var_meta_gwaa_C.cpp 79;" d file:
+INT const.h 11;" d
+INT fvlib/const.h 11;" d
+INT_NAN CastUtils.cpp /^int INT_NAN;$/;" v
+INT_NAN fvlib/CastUtils.cpp /^int INT_NAN;$/;" v
+Logger Logger.h /^ Logger(int iErrorLevel) : errorLevel(iErrorLevel), enabled(true) {}$/;" f class:Logger
+Logger Logger.h /^ Logger(int iErrorLevel, bool iEnabled) : errorLevel(iErrorLevel), enabled(iEnabled) {}$/;" f class:Logger
+Logger Logger.h /^class Logger {$/;" c
+Logger fvlib/Logger.h /^ Logger(int iErrorLevel) : errorLevel(iErrorLevel), enabled(true) {}$/;" f class:Logger
+Logger fvlib/Logger.h /^ Logger(int iErrorLevel, bool iEnabled) : errorLevel(iErrorLevel), enabled(iEnabled) {}$/;" f class:Logger
+Logger fvlib/Logger.h /^class Logger {$/;" c
+MEAN VARlib/supplementary_functions.h /^ VARIABLE_TYPE MEAN[GENO_TYPES_NUM];$/;" m struct:snp_var_data
MEAN supplementary_functions.h /^ VARIABLE_TYPE MEAN[GENO_TYPES_NUM];$/;" m struct:snp_var_data
+MESSAGE_LEVEL Logger.h 16;" d
+MESSAGE_LEVEL fvlib/Logger.h 16;" d
+MethodConvStruct ITERlib/iterator_functions.h /^ struct MethodConvStruct {$/;" s
+MethodConvStruct iterator_functions.h /^ struct MethodConvStruct {$/;" s
+NAMELENGTH const.h 18;" d
+NAMELENGTH fvlib/const.h 18;" d
+NA_value VARlib/constants.h /^const VARIABLE_TYPE NA_value = -999.999; \/\/ which numeric value is ised as NA$/;" v
NA_value constants.h /^const VARIABLE_TYPE NA_value = -999.999; \/\/ which numeric value is ised as NA$/;" v
+NA_value_int VARlib/constants.h /^const int NA_value_int = -999; \/\/ which numeric value is ised as NA$/;" v
NA_value_int constants.h /^const int NA_value_int = -999; \/\/ which numeric value is ised as NA$/;" v
+PART_SIZE frutil.cpp 162;" d file:
+PART_SIZE fvlib/frutil.cpp 162;" d file:
+REPORT_EVERY convert_util.cpp 15;" d file:
+REPORT_EVERY fvlib/convert_util.cpp 15;" d file:
+RESERVEDSPACE const.h 5;" d
+RESERVEDSPACE fvlib/const.h 5;" d
+RealHandlerWrapper RealHandlerWrapper.h /^ RealHandlerWrapper(): useCount(0) {}$/;" f class:RealHandlerWrapper
+RealHandlerWrapper RealHandlerWrapper.h /^class RealHandlerWrapper {$/;" c
+RealHandlerWrapper fvlib/RealHandlerWrapper.h /^ RealHandlerWrapper(): useCount(0) {}$/;" f class:RealHandlerWrapper
+RealHandlerWrapper fvlib/RealHandlerWrapper.h /^class RealHandlerWrapper {$/;" c
+ReusableFileHandle ReusableFileHandle.h /^ ReusableFileHandle() : isOk(false),curPos(0),$/;" f class:ReusableFileHandle
+ReusableFileHandle ReusableFileHandle.h /^ ReusableFileHandle(RealHandlerWrapper *iRealHandlerWrapper, bool iIsOk,$/;" f class:ReusableFileHandle
+ReusableFileHandle ReusableFileHandle.h /^ ReusableFileHandle(const ReusableFileHandle &rfh) :$/;" f class:ReusableFileHandle
+ReusableFileHandle ReusableFileHandle.h /^class ReusableFileHandle {$/;" c
+ReusableFileHandle fvlib/ReusableFileHandle.h /^ ReusableFileHandle() : isOk(false),curPos(0),$/;" f class:ReusableFileHandle
+ReusableFileHandle fvlib/ReusableFileHandle.h /^ ReusableFileHandle(RealHandlerWrapper *iRealHandlerWrapper, bool iIsOk,$/;" f class:ReusableFileHandle
+ReusableFileHandle fvlib/ReusableFileHandle.h /^ ReusableFileHandle(const ReusableFileHandle &rfh) :$/;" f class:ReusableFileHandle
+ReusableFileHandle fvlib/ReusableFileHandle.h /^class ReusableFileHandle {$/;" c
+SD VARlib/supplementary_functions.h /^ VARIABLE_TYPE SD[GENO_TYPES_NUM];$/;" m struct:snp_var_data
SD supplementary_functions.h /^ VARIABLE_TYPE SD[GENO_TYPES_NUM];$/;" m struct:snp_var_data
-SMV_BARTLETT_TEST_H var_homogeneity_tests.h 2;" d
+SHORT_INT const.h 9;" d
+SHORT_INT fvlib/const.h 9;" d
+SHORT_INT_NAN CastUtils.cpp /^short int SHORT_INT_NAN;$/;" v
+SHORT_INT_NAN fvlib/CastUtils.cpp /^short int SHORT_INT_NAN;$/;" v
+SIGNED_CHAR const.h 14;" d
+SIGNED_CHAR fvlib/const.h 14;" d
+SMV_CONSTANTS_H VARlib/constants.h 3;" d
SMV_CONSTANTS_H constants.h 3;" d
+SMV_DOMETA_C_H VARlib/inverse_variance_metaanalysis.h 19;" d
SMV_DOMETA_C_H inverse_variance_metaanalysis.h 19;" d
+SMV_GTPS_CONTAINER_H VARlib/gtps_container.h 19;" d
SMV_GTPS_CONTAINER_H gtps_container.h 19;" d
+SMV_SUPPLEMENTARY_FUNCTIONS_H VARlib/supplementary_functions.h 19;" d
SMV_SUPPLEMENTARY_FUNCTIONS_H supplementary_functions.h 19;" d
+SMV_VAR_HOMOGENEITY_TESTS_H VARlib/var_homogeneity_tests.h 2;" d
+SMV_VAR_HOMOGENEITY_TESTS_H var_homogeneity_tests.h 2;" d
+Snp_store_type VARlib/supplementary_functions.h /^typedef std::map<std::string, snp_var_data*> Snp_store_type; \/\/use std::string as key because for some reason it doesn't want to work with const char*$/;" t
Snp_store_type supplementary_functions.h /^typedef std::map<std::string, snp_var_data*> Snp_store_type; \/\/use std::string as key because for some reason it doesn't want to work with const char*$/;" t
+Transposer Transposer.h /^Transposer(){ square_size =10000;};$/;" f class:Transposer
+Transposer Transposer.h /^Transposer(int opt_square_size){ square_size=opt_square_size;};$/;" f class:Transposer
+Transposer Transposer.h /^class Transposer$/;" c
+Transposer fvlib/Transposer.h /^Transposer(){ square_size =10000;};$/;" f class:Transposer
+Transposer fvlib/Transposer.h /^Transposer(int opt_square_size){ square_size=opt_square_size;};$/;" f class:Transposer
+Transposer fvlib/Transposer.h /^class Transposer$/;" c
+UNSIGNED_CHAR const.h 15;" d
+UNSIGNED_CHAR fvlib/const.h 15;" d
+UNSIGNED_CHAR_NAN CastUtils.cpp /^unsigned char UNSIGNED_CHAR_NAN;$/;" v
+UNSIGNED_CHAR_NAN fvlib/CastUtils.cpp /^unsigned char UNSIGNED_CHAR_NAN;$/;" v
+UNSIGNED_INT const.h 10;" d
+UNSIGNED_INT fvlib/const.h 10;" d
+UNSIGNED_INT_NAN CastUtils.cpp /^unsigned int UNSIGNED_INT_NAN;$/;" v
+UNSIGNED_INT_NAN fvlib/CastUtils.cpp /^unsigned int UNSIGNED_INT_NAN;$/;" v
+UNSIGNED_SHORT_INT const.h 8;" d
+UNSIGNED_SHORT_INT fvlib/const.h 8;" d
+UNSIGNED_SHORT_INT_NAN CastUtils.cpp /^unsigned short int UNSIGNED_SHORT_INT_NAN;$/;" v
+UNSIGNED_SHORT_INT_NAN fvlib/CastUtils.cpp /^unsigned short int UNSIGNED_SHORT_INT_NAN;$/;" v
+VARIABLE_TYPE VARlib/supplementary_functions.h 38;" d
+VARIABLE_TYPE VARlib/var_meta_gwaa_C.cpp 78;" d file:
VARIABLE_TYPE supplementary_functions.h 38;" d
VARIABLE_TYPE var_meta_gwaa_C.cpp 78;" d file:
+WRITE_SPEED_PROPORTION AbstractMatrix.h 12;" d
+WRITE_SPEED_PROPORTION fvlib/AbstractMatrix.h 12;" d
+Z VARlib/supplementary_functions.h /^ double Z; \/\/homogeneity test$/;" m struct:snp_var_data
Z supplementary_functions.h /^ double Z; \/\/homogeneity test$/;" m struct:snp_var_data
+Z_2df VARlib/supplementary_functions.h /^ double Z_2df; \/\/homogeneity test 2df only$/;" m struct:snp_var_data
Z_2df supplementary_functions.h /^ double Z_2df; \/\/homogeneity test 2df only$/;" m struct:snp_var_data
+_ VARlib/inverse_variance_metaanalysis.cpp 30;" d file:
+_ VARlib/inverse_variance_metaanalysis.cpp 33;" d file:
+_ VARlib/var_homogeneity_test_C.cpp 34;" d file:
+_ VARlib/var_homogeneity_test_C.cpp 37;" d file:
+_ VARlib/var_meta_gwaa_C.cpp 71;" d file:
+_ VARlib/var_meta_gwaa_C.cpp 74;" d file:
_ inverse_variance_metaanalysis.cpp 30;" d file:
_ inverse_variance_metaanalysis.cpp 33;" d file:
_ var_homogeneity_test_C.cpp 34;" d file:
_ var_homogeneity_test_C.cpp 37;" d file:
_ var_meta_gwaa_C.cpp 71;" d file:
_ var_meta_gwaa_C.cpp 74;" d file:
+__AbstractMatrix__ AbstractMatrix.h 2;" d
+__AbstractMatrix__ fvlib/AbstractMatrix.h 2;" d
+__CONST_H__ const.h 2;" d
+__CONST_H__ fvlib/const.h 2;" d
+__CONVERT_UTIL__ convert_util.h 2;" d
+__CONVERT_UTIL__ fvlib/convert_util.h 2;" d
+__CastUtils__ CastUtils.h 2;" d
+__CastUtils__ fvlib/CastUtils.h 2;" d
+__DAUTIL_H__ DAlib/dautil.h 2;" d
+__DAUTIL_H__ dautil.h 2;" d
+__FRUTIL__ frutil.h 2;" d
+__FRUTIL__ fvlib/frutil.h 2;" d
+__FRVECTOR__ FileVector.h 2;" d
+__FRVECTOR__ fvlib/FileVector.h 2;" d
+__FRVERSION__ frversion.h 2;" d
+__FRVERSION__ fvlib/frversion.h 2;" d
+__FilteredMatrix__ FilteredMatrix.h 2;" d
+__FilteredMatrix__ fvlib/FilteredMatrix.h 2;" d
+__ITERATOR_FUNCTIONS_H__ ITERlib/iterator_functions.h 2;" d
+__ITERATOR_FUNCTIONS_H__ iterator_functions.h 2;" d
+__LOGGER__ Logger.h 2;" d
+__LOGGER__ fvlib/Logger.h 2;" d
+__RSTAFF_H__ DAlib/Rstaff.h 2;" d
+__RSTAFF_H__ Rstaff.h 2;" d
+__RealHandlerWrapper__ RealHandlerWrapper.h 2;" d
+__RealHandlerWrapper__ fvlib/RealHandlerWrapper.h 2;" d
+__ReusableFileHandle__ ReusableFileHandle.h 2;" d
+__ReusableFileHandle__ fvlib/ReusableFileHandle.h 2;" d
+___TRANSPOSE___ Transposer.h 2;" d
+___TRANSPOSE___ fvlib/Transposer.h 2;" d
+addVariable FileVector.cpp /^void FileVector::addVariable(void *invec, string varName) {$/;" f class:FileVector
+addVariable FilteredMatrix.cpp /^void FilteredMatrix::addVariable(void * invec, string varname) {$/;" f class:FilteredMatrix
+addVariable fvlib/FileVector.cpp /^void FileVector::addVariable(void *invec, string varName) {$/;" f class:FileVector
+addVariable fvlib/FilteredMatrix.cpp /^void FilteredMatrix::addVariable(void * invec, string varname) {$/;" f class:FilteredMatrix
+addVariableAs AbstractMatrix.h /^ void addVariableAs(DT * outvec, string varname)$/;" f class:AbstractMatrix
+addVariableAs fvlib/AbstractMatrix.h /^ void addVariableAs(DT * outvec, string varname)$/;" f class:AbstractMatrix
+all Logger.cpp 6;" d file:
+all fvlib/Logger.cpp 6;" d file:
+analysis_type_enum VARlib/supplementary_functions.h /^enum analysis_type_enum {AAvsABvsBB, AAvsABandBB, ABvsAAandBB, BBvsAAandAB};$/;" g
analysis_type_enum supplementary_functions.h /^enum analysis_type_enum {AAvsABvsBB, AAvsABandBB, ABvsAAandBB, BBvsAAandAB};$/;" g
-bartlett_test var_homogeneity_tests.cpp /^double bartlett_test(snp_var_data * snp, bool all_genogroup_only)$/;" f
-bartlett_test var_homogeneity_tests.cpp /^double bartlett_test(std::list<my_small_vector> * samples, bool all_genogroup_only)$/;" f
-break_trait_up_into_groups supplementary_functions.cpp /^void break_trait_up_into_groups(std::list<my_small_vector> *trait_groups, int* snp, double *trait, unsigned* nids, char* analys_type_, int * is_trait_na)$/;" f
+assignDoubleMatrix AbstractMatrix_R.cpp /^ SEXP assignDoubleMatrix(SEXP ptr, SEXP obsIndexes, SEXP varIndexes, SEXP values, SEXP direction){$/;" f
+assignDoubleMatrix DAlib/AbstractMatrix_R.cpp /^ SEXP assignDoubleMatrix(SEXP ptr, SEXP obsIndexes, SEXP varIndexes, SEXP values, SEXP direction){$/;" f
+bartlett VARlib/supplementary_functions.h /^enum testname_enum {bartlett, levene, likelihood, kolmogorov_smirnov};$/;" e enum:testname_enum
+bartlett supplementary_functions.h /^enum testname_enum {bartlett, levene, likelihood, kolmogorov_smirnov};$/;" e enum:testname_enum
+bartlett_test VARlib/var_homogeneity_tests.cpp /^chisq_df bartlett_test(snp_var_data * snp)$/;" f
+bartlett_test VARlib/var_homogeneity_tests.cpp /^chisq_df bartlett_test(std::list<my_small_vector> * samples)$/;" f
+bartlett_test var_homogeneity_tests.cpp /^chisq_df bartlett_test(snp_var_data * snp)$/;" f
+bartlett_test var_homogeneity_tests.cpp /^chisq_df bartlett_test(std::list<my_small_vector> * samples)$/;" f
+bitsPerRecord frutil.h /^ unsigned int bitsPerRecord;$/;" m class:FileHeader
+bitsPerRecord fvlib/frutil.h /^ unsigned int bitsPerRecord;$/;" m class:FileHeader
+blockWriteOrRead RealHandlerWrapper.cpp /^void RealHandlerWrapper::blockWriteOrRead(unsigned long iLength, char* data, bool writeAction) {$/;" f class:RealHandlerWrapper
+blockWriteOrRead ReusableFileHandle.cpp /^void ReusableFileHandle::blockWriteOrRead(unsigned long length, char* data, bool writeAction){$/;" f class:ReusableFileHandle
+blockWriteOrRead frutil.cpp /^void blockWriteOrRead(fstream& file, unsigned long length, char* data, bool writeAction){$/;" f
+blockWriteOrRead fvlib/RealHandlerWrapper.cpp /^void RealHandlerWrapper::blockWriteOrRead(unsigned long iLength, char* data, bool writeAction) {$/;" f class:RealHandlerWrapper
+blockWriteOrRead fvlib/ReusableFileHandle.cpp /^void ReusableFileHandle::blockWriteOrRead(unsigned long length, char* data, bool writeAction){$/;" f class:ReusableFileHandle
+blockWriteOrRead fvlib/frutil.cpp /^void blockWriteOrRead(fstream& file, unsigned long length, char* data, bool writeAction){$/;" f
+break_trait_up_into_groups VARlib/supplementary_functions.cpp /^void break_trait_up_into_groups(std::list<my_small_vector> *trait_groups, int* snp, double *trait, unsigned* nids, analysis_type_enum analys_type, int * is_trait_na)$/;" f
+break_trait_up_into_groups supplementary_functions.cpp /^void break_trait_up_into_groups(std::list<my_small_vector> *trait_groups, int* snp, double *trait, unsigned* nids, analysis_type_enum analys_type, int * is_trait_na)$/;" f
+bufToString CastUtils.cpp /^string bufToString(short int dataType, char *data, string nanString){$/;" f
+bufToString fvlib/CastUtils.cpp /^string bufToString(short int dataType, char *data, string nanString){$/;" f
+bytesPerRecord frutil.h /^ unsigned int bytesPerRecord;$/;" m class:FileHeader
+bytesPerRecord fvlib/frutil.h /^ unsigned int bytesPerRecord;$/;" m class:FileHeader
+cacheAllNames FileVector.cpp /^void FileVector::cacheAllNames(bool doCache) {$/;" f class:FileVector
+cacheAllNames FilteredMatrix.cpp /^void FilteredMatrix::cacheAllNames(bool doCache) {$/;" f class:FilteredMatrix
[TRUNCATED]
To get the complete diff run:
svnlook diff /svnroot/genabel -r 625
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