build_command.php:// --- Input/Output Section -------------------------------------------------------------- build_command.php: if ($file) { $cmdline .= " --file ".$file; } build_command.php: elseif ($bfile) { $cmdline .= " --bfile ".$bfile; } build_command.php: elseif ($ped && $map) { $cmdline .= " --ped ".$ped." --map ".$map; } build_command.php: elseif ($bed && $bim && $fam) { $cmdline .= " --bed ".$bed." --bim ".$bim." --fam ".$fam; } build_command.php: { $cmdline .= " --out ".$out;} build_command.php:// --- End of Input/Output Section ------------------------------------------------------- build_command.php:// --- Data Management Section ----------------------------------------------------------- build_command.php: if ($m=="recode") $cmdline .= " --recode"; build_command.php: if ($m=="recode12") $cmdline .= " --recode12"; build_command.php: if ($m=="recodeAD") $cmdline .= " --recodeAD"; build_command.php: if ($m=="makebed") $cmdline .= " --make-bed"; build_command.php: $cmdline .= " --merge ".$mergeped." ".$mergemap." --merge-mode ".$mmode; build_command.php: if ($m=="extract") $cmdline .= " --extract ".$extract; build_command.php: if ($m=="exclude") $cmdline .= " --exclude ".$exclude; build_command.php: if ( $m=="keep") $cmdline .= " --keep ".$keep; build_command.php: if ($m=="remove") $cmdline .= " --remove ".$remove; build_command.php: if ($m=="flip") $cmdline .= " --flip ".$flip; build_command.php: if ($p=="1") $cmdline .= " --recode"; build_command.php: if ($p=="2") $cmdline .= " --make-bed"; build_command.php:// --- End of Data Management Section ---------------------------------------------------- build_command.php:// --- Summary Stats Section ------------------------------------------------------------- build_command.php: if ($m=="missing") { $cmdline .= " --missing"; } build_command.php: if ($m=="test-missing") { $cmdline .= " --test-missing"; } build_command.php: if ($m=="freq") { $cmdline .= " --freq"; } build_command.php: if ($m=="hardy") { $cmdline .= " --hardy "; } build_command.php: if ($m=="mendel") { $cmdline .= " --mendel ";} build_command.php:// --- End of Summary Stats Section ------------------------------------------------------ build_command.php:// --- Population Stratification Section-------------------------------------------------- build_command.php: $cmdline .= " --cluster"; build_command.php: if ($pmerge) {$cmdline .= " --pmerge ".$pmerge;} build_command.php: if ($matrix) $cmdline .= " --matrix"; build_command.php: if ($match) {$cmdline .= " --match ".$match;} build_command.php: if ($matchtype) {$cmdline .= " --match-type".$matchtype;} build_command.php: if ($qmatch && $qt) {$cmdline .= " --qmatch ".$qmatch." --qt ".$qt;} build_command.php: if ($m=="genome") $cmdline .= " --genome --min " .$min; build_command.php: if ($m=="inbreeding") $cmdline .= " --het "; build_command.php: if ($m=="homo-run-snps") $cmdline .= " --homo-run-snps " .$homo_run_snps; build_command.php:// --- End of Population Stratification Section------------------------------------------- build_command.php:// --- Linkage Disequilibrium Section-------------------------------------------------- build_command.php: { $cmdline .= " --r"; } build_command.php: { $cmdline .= " --r2"; } build_command.php: if ($hap) {$cmdline .= " --hap ".$hap;} build_command.php: { $cmdline .= " --hapfreq"; } build_command.php: { $cmdline .= " --phase"; } build_command.php: { $cmdline .= " --hapfreq"; } build_command.php: $cmdline .= " --impute --pp ".$pp; build_command.php:// --- End of Linkage Disequilibrium Section------------------------------------------- build_command.php:// --- Association Analysis/Single SNP Section----------------------------------------- build_command.php: if ($m=="assoc") { $cmdline .= " --assoc"; } build_command.php: if ($m=="model") { $cmdline .= " --model"; } build_command.php: if ($m=="qt") { $cmdline .= " --assoc"; } build_command.php: $cmdline .= " --perm"; build_command.php: //$cmdline .= " --aperm ".$minperm." ".$maxperm." ".$alpha." ".$ci." ".$intercept." ".$slope; build_command.php: $cmdline .= " --mperm ".$mperm; build_command.php: if ($m=="mh1") { $cmdline .= " --mh1"; } build_command.php: if ($m=="mh2") { $cmdline .= " --mh2"; } build_command.php: if ($homog==1) { $cmdline .= " --bd"; } build_command.php: elseif ($homog==2) { $cmdline .= " --homog"; } build_command.php: if ($within && !$family) { $cmdline .= " --within ".$within; } build_command.php: elseif ($family && !$within) { $cmdline .= " --family"; } build_command.php: else {$errcnt++; echo "Error: choose exactly one of --within or --family.
";} build_command.php: { $cmdline .= " --tdt"; } build_command.php: { $cmdline .= " --parentdt1"; } build_command.php: { $cmdline .= " --parentdt2"; } build_command.php: if ($m=="qtdt") { $cmdline .= " --genedrop"; } build_command.php:// --- End of Association Analysis/Single SNP Section---------------------------------- build_command.php:// --- Association Analysis/Epistatic Analysis Section--------------------------------- build_command.php: $cmdline .= " --epistasis"; build_command.php: $cmdline .= " --case-only"; build_command.php: { $cmdline .= " --set ".$set;} build_command.php: { $cmdline .= " --set ".$set ." --set-by-all";} build_command.php: { $cmdline .= " --set ".$set;} build_command.php: $cmdline .= " --epi1 ".$epi1; build_command.php: $cmdline .= " --epi2 ".$epi2; build_command.php: $cmdline .= " --genepi --R"; build_command.php: if ($p==1) { $cmdline .= " --case-only"; } build_command.php: $cmdline .= " --set ".$set; build_command.php: $cmdline .= " --perm ".$perm; build_command.php:// --- End of Association Analysis/Epistatic Analysis Section-------------------------- build_command.php:// --- Sel Global Variable Section ---------------------------------------------------- build_command.php: if ($mind) {$cmdline .= " --mind " .$mind;} build_command.php: if ($geno) {$cmdline .= " --geno " .$geno;} build_command.php: if ($maf) {$cmdline .= " --maf " .$maf;} build_command.php: $cmdline .= " --cell " .$cell; build_command.php: $cmdline .= " --hwe " .$hwe; build_command.php: $cmdline .= " --me ".$ime ." " .$fme; build_command.php:// --- End Sel Global Variable Section ------------------------------------------------ desc_analysis.php: $input .= "-->Create new PED/MAP fileset (reordered)
"; desc_analysis.php: $input .= "---->Preserve original allele coding
"; desc_analysis.php: $input .= "-->Create new PED/MAP fileset (reordered)
"; desc_analysis.php: $input .= "---->Recode genotypes 11, 12 and 22 (00 missing)
"; desc_analysis.php: $input .= "-->Create a binary bED fileset
"; desc_analysis.php: $input .= "-->Merge two PED files
"; desc_analysis.php: $input .= "-->Extract a subset of SNPs
"; desc_analysis.php: $input .= "-->Exclude a subset of SNPs
"; desc_analysis.php: $input .= "-->Extract a subset of individuals
"; desc_analysis.php: $input .= "-->Exclude of subset of individuals
"; desc_analysis.php: $input .= "-->Flip SNP strand
"; desc_analysis.php: if ($p==1) {$input .= "---->Output standard PED/MAP fileset
";} desc_analysis.php: elseif ($p==2) {$input .= "---->Output a binary bED fileset
";} desc_analysis.php: $input .= "-->Missingness rates
"; desc_analysis.php: $input .= "---->SNP and individual missing rates
"; desc_analysis.php: $input .= "-->Missingness rates
"; desc_analysis.php: $input .= "---->Test for different rates between cases and controls
"; desc_analysis.php: $input .= "-->Allele frequencies
"; desc_analysis.php: $input .= "-->Hardy-Weinberg equilibrium tests
"; desc_analysis.php: $input .= "---->Ignore phenotype
"; desc_analysis.php: $input .= "-->Hardy-Weinberg equilibrium tests
"; desc_analysis.php: $input .= "---->Stratify by case/control statues
"; desc_analysis.php: $input .= "-->Mendel error rates for nuclear family data
"; in_and_out.php: $input .= "-->Create new PED/MAP fileset (reordered)
"; in_and_out.php: $input .= "---->Preserve original allele coding
"; in_and_out.php: $input .= "-->Create new PED/MAP fileset (reordered)
"; in_and_out.php: $input .= "---->Recode genotypes 11, 12 and 22 (00 missing)
"; in_and_out.php: $input .= "-->Create new PED/MAP fileset (reordered)
"; in_and_out.php: $input .= "---->Recode genotypes as additive and dominant components
"; in_and_out.php: $input .= "-->Create a binary bED fileset
"; in_and_out.php: $input .= "-->Merge two PED files
"; in_and_out.php: $input .= "-->Extract a subset of SNPs
"; in_and_out.php: $input .= "-->Exclude a subset of SNPs
"; in_and_out.php: $input .= "-->Extract a subset of individuals
"; in_and_out.php: $input .= "-->Exclude of subset of individuals
"; in_and_out.php: $input .= "-->Flip SNP strand
"; in_and_out.php: $input .= "---->Output standard PED/MAP fileset
"; in_and_out.php: $input .= "---->Output a binary bED fileset
"; in_and_out.php: $input .= "-->Missingness rates
"; in_and_out.php: $input .= "---->SNP and individual missing rates
"; in_and_out.php: $input .= "-->Missingness rates
"; in_and_out.php: $input .= "---->Test for different rates between cases and controls
"; in_and_out.php: $input .= "-->Allele frequencies
"; in_and_out.php: $input .= "-->Hardy-Weinberg equilibrium tests
"; in_and_out.php: if ($p==1) {$input .= "---->Ignore phenotype
"; } in_and_out.php: elseif ($p==2) {$input .= "---->Stratify by case/control statues
";} in_and_out.php: $input .= "-->Mendel error rates for nuclear family data
"; in_and_out.php: $input .= "-->IBS distance-based clustering
"; in_and_out.php: $input .= "---->Cluster on genome-wide IBS
"; in_and_out.php: $input .= "-->IBS distance-based clustering
"; in_and_out.php: $input .= "---->Cluster on genome-wide IBS and external matching criteria
"; in_and_out.php: $input .= "-->IBD estimation (genome-wide)
"; in_and_out.php: $input .= "-->Heterozygosity / inbreeding coefficients
"; in_and_out.php: $input .= "-->Runs of homozygosity
"; in_and_out.php: $input .= "-->Pairwise r and r-squared
"; in_and_out.php: $input .= "-->haplotype inference
"; in_and_out.php: $input .= "---->Calculate haplotype frequencies
"; in_and_out.php: $input .= "-->haplotype inference
"; in_and_out.php: $input .= "---->List individuals' haplotype phases
"; in_and_out.php: $input .= "-->haplotype inference
"; in_and_out.php: $input .= "---->Test case/control haplotype association
"; in_and_out.php: $input .= "-->haplotype inference
"; in_and_out.php: $input .= "---->Create imputed most-likely haplotype dataset
"; in_and_out.php: $input .="-->Single SNP analyses
"; in_and_out.php: $input .="---->Population based sample
"; in_and_out.php: $input .="------>Disease trait
"; in_and_out.php: $input .="-------->Basic allelic test
"; in_and_out.php: $input .="---------->Without permutation
"; in_and_out.php: $input .="---------->With adaptive permutation
"; in_and_out.php: $input .="---------->With maxT permutation
"; in_and_out.php: $input .="-->Single SNP analyses
"; in_and_out.php: $input .="---->Population based sample
"; in_and_out.php: $input .="------>Disease trait
"; in_and_out.php: $input .="-------->Cochran-Armitage trend test and genotypic test
"; in_and_out.php: $input .="---------->Without permutation
"; in_and_out.php: $input .="---------->With adaptive permutation
"; in_and_out.php: $input .="---------->With maxT permutation
"; in_and_out.php: $input .="-->Single SNP analyses
"; in_and_out.php: $input .="---->Population based sample
"; in_and_out.php: $input .="------>Disease trait
"; in_and_out.php: $input .="-------->Stratified/clustered sample tests
"; in_and_out.php: $input .="---------->Within-cluster permutation
"; in_and_out.php: $input .="-------->With adaptive permutation
"; in_and_out.php: $input .="-------->With maxT permutation
"; in_and_out.php: $input .="-->Single SNP analyses
"; in_and_out.php: $input .="---->Population based sample
"; in_and_out.php: $input .="------>Disease trait
"; in_and_out.php: $input .="-------->Stratified/clustered sample tests
"; in_and_out.php: $input .="---------->Cochran-Mantel-Haenszel tests
"; in_and_out.php: $input .="------------>SNP-disease association conditional on cluster
"; in_and_out.php: $input .="-->Single SNP analyses
"; in_and_out.php: $input .="---->Population based sample
"; in_and_out.php: $input .="------>Disease trait
"; in_and_out.php: $input .="-------->Stratified/clustered sample tests
"; in_and_out.php: $input .="---------->Cochran-Mantel-Haenszel tests
"; in_and_out.php: $input .="------------>SNP-cluster association conditional on disease
"; in_and_out.php: $input .="-->Single SNP analyses
"; in_and_out.php: $input .="---->Population based sample
"; in_and_out.php: $input .="------>Disease trait
"; in_and_out.php: $input .="-------->Stratified/clustered sample tests
"; in_and_out.php: $input .="---------->Homogeneity of odds ratio tests
"; in_and_out.php: $input .="-->Single SNP analyses
"; in_and_out.php: $input .="---->Population based sample
"; in_and_out.php: $input .="------>Quantitative trait
"; in_and_out.php: $input .="-------->Without permutation
"; in_and_out.php: $input .="-------->With adaptive permutation
"; in_and_out.php: $input .="-------->With maxT permutation
"; in_and_out.php: $input .="-->Single SNP analyses
"; in_and_out.php: $input .="---->Population based sample
"; in_and_out.php: $input .="------>Within-cluster permutation
"; in_and_out.php: $input .="-------->With adaptive permutation
"; in_and_out.php: $input .="-------->With maxT permutation
"; in_and_out.php:// --- Association Analysis/Single SNP analyses/Family-based Sample ----------------- in_and_out.php: $input .= "-->Single SNP analyses
"; in_and_out.php: $input .= "---->Family-based sample
"; in_and_out.php: $input .= "------>Disease traits: TDT analysis
"; in_and_out.php: if ($set=="no") { $input .= "-------->Single SNP TDT only
";} in_and_out.php: elseif ($set=="true") { $input .= "-------->Single SNP and set-based TDT
";} in_and_out.php: $input .= "-->Single SNP analyses
"; in_and_out.php: $input .= "---->Family-based sample
"; in_and_out.php: $input .= "------>Quantitative trait: gene-dropping permutation
"; in_and_out.php: if ($p==1) {$input .= "-------->Gene-drop from founders
";} in_and_out.php: if ($p==2) {$input .= "-------->Gene-drop from parents
";} in_and_out.php:// ----- Epistatic Analysis ------------------------------------------------- in_and_out.php: $input .= "-->Epistatic analyses
"; in_and_out.php: $input .= "---->SNP x SNP epistasis
"; in_and_out.php: $input .= "-->Epistatic analyses
"; in_and_out.php: $input .= "---->Gene-based epistasis
"; in_and_out.php: if ($p==1) {$input .= "------>Case-only analysis
";} in_and_out.php: elseif ($p==2) {$input .= "------>Case/control analysis
";} pom1a.php: pom1b.php: pom1.php: pom2.php: pom2.php: --file pom2.php: --ped pom2.php: --map pom2.php: --bfile pom2.php:exist. These files are created by the --make-bed (create binary PED file) pom2.php: --bed pom2.php: --map pom2.php: --fam pom2.php: pom2.php: pom2.php: --out pom2.php: pom2.php: pom2.php: --mind pom2.php: --geno pom2.php: --maf pom2.php: --cell pom2.php:with fewer than this many genotypes in the 2x3 genotypic table (--model option) pom2.php: pom2.php: --hwe pom2.php: pom2.php: --me pom2.php: pom2.php: pom2.php: pom2.php: --merge pom2.php: --merge-mode pom2.php:Merge mode. This option specifies the behavior of the --merge pom2.php:all mismatching calls (diff mode -- do not merge); 7) Report mismatching non-missing pom2.php:calls (diff mode -- do not merge) pom2.php: --extract pom2.php: --exclude pom2.php: --keep pom2.php: --remove pom2.php: --flip pom2.php: pom2.php: pom2.php: pom2.php: pom2.php: pom2.php: pom2.php: pom2.php: --pmerge pom2.php:the --genome option. pom2.php: --matrix pom2.php: --match pom2.php: --match-type pom2.php: --qmatch pom2.php: --qt pom2.php: --min pom2.php: Minimum pi-hat to output pair. The --genome option pom2.php: --homo-run-snps pom2.php: pom2.php: pom2.php: --r
--r2 pom2.php: pom2.php: --hap pom2.php: --pp pom2.php: pom2.php: pom2.php: --mperm pom2.php: --bd
pom2.php: --homog pom2.php: Select Odds Ratio Test The --bd option selects a pom2.php:"Breslow-Day" homogeneity of odds ratios test and the --homog option selects a pom2.php: --within pom2.php: --family pom2.php: --tdt
--parentdt1 pom2.php:
--parentdt2 pom2.php: pom2.php: pom2.php: --epi1 pom2.php: --epi2 pom2.php: --set pom2.php: --set pom2.php: --perm pom2.php:test is computationally intensive -- it might not be feasible to test a large number pom2.php: pom3.php: pom3.php: pom3.php: pom3.php: pom3.php: pom3.php: pom3.php: pom3.php: pom3.php: xmltree.orig.php: $this->treeDepth--; xmltree.orig.php: $this->xmlDepth[$parser]--; xmltree.orig.php: for ($i=$this->nodeCount-1; $i>=0; $i--) { xmltree.php: $this->treeDepth--; xmltree.php: $this->xmlDepth[$parser]--; xmltree.php: for ($i=$this->nodeCount-1; $i>=0; $i--) { xmltree.php: for ($i=$this->nodeCount-1; $i>=0; $i--) {