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: