";
$input .= "-->Create new PED/MAP fileset (reordered)
";
$input .= "---->Preserve original allele coding
";
$warning .= "";
$output .= "
" .$out."-recode.ped | ";
$output .= "Recoded PED file |
";
$output .= "".$out."-recode.map | ";
$output .= "Recoded MAP file |
";
}
if ($m=="recode12")
{
$input .= "Data management
";
$input .= "-->Create new PED/MAP fileset (reordered)
";
$input .= "---->Recode genotypes 11, 12 and 22 (00 missing)
";
$output .= "" .$out."-recode.ped | ";
$output .= "Recoded PED file |
";
$output .= "" .$out."-recode.map | ";
$output .= "Recoded MAP file |
";
}
if ($m=="recodeAD")
{
$input .= "Data management
";
$input .= "-->Create new PED/MAP fileset (reordered)
";
$input .= "---->Recode genotypes as additive and dominant components
";
$output .= "" .$out."-recode.raw | ";
$output .= "Recoded raw data file |
";
}
if ($m=="makebed")
{
$input .= "Data management
";
$input .= "-->Create a binary bED fileset
";
$output .= "" .$out.".bed | ";
$output .= " Binary PED file |
";
$output .= "" .$out.".bim | ";
$output .= " Binary MAP file |
";
$output .= "" .$out.".fam | ";
$output .= " Binary FAM file |
";
}
if ($m=="merge" || $m=="mmerge")
{
$input .= "Data management
";
$input .= "-->Merge two PED files
";
if ($m=="mmerge" || ($mmode>=1 && $mmode<=5))
{
if ($p==1)
{
$output .= "" .$out."-recode.ped | ";
$output .= "Recoded PED file |
";
$output .= "".$out."-recode.map | ";
$output .= "Recoded MAP file |
";
}
elseif ($p==2)
{
$output .= "" .$out.".bed | ";
$output .= " Binary PED file |
";
$output .= "" .$out.".bim | ";
$output .= " Binary MAP file |
";
$output .= "" .$out.".fam | ";
$output .= " Binary FAM file |
";
}
}
elseif ($mmode==6 || $mmode==7)
{
$output .= "" .$out.".diff | ";
$output .= "Difference file |
";
}
}
if ($m=="extract")
{
$input .= "Data management
";
$input .= "-->Extract a subset of SNPs
";
}
if ($m=="exclude")
{
$input .= "Data management
";
$input .= "-->Exclude a subset of SNPs
";
}
if ($m=="keep")
{
$input .= "Data management
";
$input .= "-->Extract a subset of individuals
";
}
if ($m=="remove")
{
$input .= "Data management
";
$input .= "-->Exclude of subset of individuals
";
}
if ($m=="flip")
{
$input .= "Data management
";
$input .= "-->Flip SNP strand
";
}
if ($m=="extract" || $m=="exclude" || $m=="keep" || $m=="remove" || $m=="flip")
{
if ($p==1)
{
$input .= "---->Output standard PED/MAP fileset
";
$output .= "" .$out."-recode.ped | ";
$output .= "Recoded PED file |
";
$output .= "" .$out."-recode.map | ";
$output .= "Recoded MAP file |
";
}
elseif ($p==2)
{
$input .= "---->Output a binary bED fileset
";
$output .= "" .$out.".bed | ";
$output .= "Binary PED file |
";
$output .= "" .$out.".bim | ";
$output .= "Binary MAP file |
";
$output .= "" .$out.".fam | ";
$output .= "Binary FAM file |
";
}
}
//_____End Data Management______________________________________________________________
//_____Summary Statistics_______________________________________________________________
if ($m=="missing")
{
$input .= "Summary statistics
";
$input .= "-->Missingness rates
";
$input .= "---->SNP and individual missing rates
";
$output .= "" .$out.".imiss | ";
$output .= "Missing rates, per individual |
";
$output .= "" .$out.".lmiss | ";
$output .= "Missing rates, per locus |
";
}
if ($m=="test-missing")
{
$input .= "Summary statistics
";
$input .= "-->Missingness rates
";
$input .= "---->Test for different rates between cases and controls
";
$output .= "" .$out.".missing | ";
$output .= "Test of differences in C/C missing rates |
";
}
if ($m=="freq")
{
$input .= "Summary statistics
";
$input .= "-->Allele frequencies
";
$output .= "" .$out.".frq | ";
$output .= "Allele frequency table |
";
}
if ($m=="hardy")
{
$input .= "Summary statistics
";
$input .= "-->Hardy-Weinberg equilibrium tests
";
$output .= "" .$out.".hwe | ";
$output .= "Hardy-Weinberg test statistics |
";
if ($p==1) {$input .= "---->Ignore phenotype
"; }
elseif ($p==2) {$input .= "---->Stratify by case/control statues
";}
}
if ($m=="mendel")
{
$input .= "Summary statistics
";
$input .= "-->Mendel error rates for nuclear family data
";
$output .= "" .$out.".mendel | ";
$output .= "Mendel errors, per error |
";
$output .= "" .$out.".imendel | ";
$output .= "Mendel errors, per individual |
";
$output .= "" .$out.".fmendel | ";
$output .= "Mendel errors, per family |
";
$output .= "" .$out.".lmendel | ";
$output .= "Mendel errors, per locus |
";
}
//_____End Summary Statistics___________________________________________________________
//_____Population Stratification________________________________________________________
if ($m=="cluster" && $p==1)
{
$input .= "Population stratification and matching
";
$input .= "-->IBS distance-based clustering
";
$input .= "---->Cluster on genome-wide IBS
";
$output .= "".$out.".cluster0 | ";
$output .= "Progress of IBS clustering |
";
$output .= "".$out.".cluster1 | ";
$output .= "IBS cluster solution, format 1 |
";
$output .= "".$out.".cluster2 | ";
$output .= "IBS cluster solution, format 2 |
";
$output .= "".$out.".cluster3 | ";
$output .= "IBS cluster solution, format 3 |
";
}
if ($m=="cluster" && $p==2)
{
$input .= "Population stratification and matching
";
$input .= "-->IBS distance-based clustering
";
$input .= "---->Cluster on genome-wide IBS and external matching criteria
";
$output .= "".$out.".cluster0 | ";
$output .= "Progress of IBS clustering |
";
$output .= "".$out.".cluster1 | ";
$output .= "IBS cluster solution, format 1 |
";
$output .= "".$out.".cluster2 | ";
$output .= "IBS cluster solution, format 2 |
";
$output .= "".$out.".cluster3 | ";
$output .= "IBS cluster solution, format 3 |
";
}
if ($m=="cluster" && $matrix)
{
$output .= "".$out.".mdist | ";
$output .= "IBS distance matrix |
";
}
if ($m=="genome")
{
$input .= "Population stratification and matching
";
$input .= "-->IBD estimation (genome-wide)
";
$output .= "" .$out.".genome | ";
$output .= "Genome-wide IBD/IBS pairwise measures |
";
}
if ($m=="inbreeding")
{
$input .= "Population stratification and matching
";
$input .= "-->Heterozygosity / inbreeding coefficients
";
$output .= "" .$out.".het | ";
$output .= "Individual inbreeding coefficients |
";
}
if ($m=="homo-run-snps")
{
$input .= "Population stratification and matching
";
$input .= "-->Runs of homozygosity
";
$output .= "" .$out.".hom | ";
$output .= "Runs of homozygosity |
";
}
//_____End Population Stratification____________________________________________________
//_____Linkage Disequilibrium___________________________________________________________
if ($m=="ld-r")
{
$input .= "Linkage disequilibrium and haplotype inference
";
$input .= "-->Pairwise r and r-squared
";
if ($ld==1)
{
$output .= "" .$out.".ld | ";
$output .= "Pairwise LD (genotype correlation) |
";
}
elseif ($ld==2)
{
$output .= "" .$out.".ld | ";
$output .= "Pairwise LD (squared genotype correlation) |
";
}
}
if ($m=="hap" && $p==1)
{
$input .= "Linkage disequilibrium and haplotype inference
";
$input .= "-->haplotype inference
";
$input .= "---->Calculate haplotype frequencies
";
$output .= "" .$out.".freq.hap | ";
$output .= "Haplotype frequencies (and C/C test) |
";
}
if ($m=="hap" && $p==2)
{
$input .= "Linkage disequilibrium and haplotype inference
";
$input .= "-->haplotype inference
";
$input .= "---->List individuals' haplotype phases
";
$output .= "" .$out.".phase-* | ";
$output .= "Haplotype phases (one file per locus) |
";
}
if ($m=="hap" && $p==3)
{
$input .= "Linkage disequilibrium and haplotype inference
";
$input .= "-->haplotype inference
";
$input .= "---->Test case/control haplotype association
";
$output .= "" .$out.".assoc.hap | ";
$output .= "Haplotype frequencies (and C/C test) |
";
}
if ($m=="hap" && $p==4)
{
$input .= "Linkage disequilibrium and haplotype inference
";
$input .= "-->haplotype inference
";
$input .= "---->Create imputed most-likely haplotype dataset
";
$output .= "" .$out."-impute.ped | ";
$output .= "PED file of imputed SNPs |
";
$output .= "" .$out."-impute.map | ";
$output .= "MAP file of imputed SNPs |
";
}
//_____End Linkage Disequilibrium_______________________________________________________
//_____Association Analysis_____________________________________________________________
if ($m=="assoc")
{
$input .="Association analysis
";
$input .="-->Single SNP analyses
";
$input .="---->Population based sample
";
$input .="------>Disease trait
";
$input .="-------->Basic allelic test
";
if ($p==1)
{
$input .="---------->Without permutation
";
$output .= "" .$out.".assoc | ";
$output .= "Association results |
";
}
elseif ($p==2)
{
$input .="---------->With adaptive permutation
";
$output .= "" .$out.".assoc.perm | ";
$output .= "Adaptive permutation empirical p-values |
";
}
elseif ($p==3)
{
$input .="---------->With maxT permutation
";
$output .= "" .$out.".assoc.mperm | ";
$output .= " maxT permutation empirical p-values |
";
}
}
if ($m=="model")
{
$input .="Association analysis
";
$input .="-->Single SNP analyses
";
$input .="---->Population based sample
";
$input .="------>Disease trait
";
$input .="-------->Cochran-Armitage trend test and genotypic test
";
if ($p==1)
{
$input .="---------->Without permutation
";
$output .= "" .$out.".model | ";
$output .= " Full-model association results |
";
}
elseif ($p==2)
{
$input .="---------->With adaptive permutation
";
$output .= "" .$out.".model | ";
$output .= "Full-model association results |
";
$output .= "" .$out.".model.perm | ";
$output .= "Empirical significance values |
";
}
elseif ($p==3)
{
$input .="---------->With maxT permutation
";
$output .= "" .$out.".model | ";
$output .= "Full-model association results |
";
$output .= "" .$out.".model.mperm | ";
$output .= "Empirical significance values |
";
}
}
if ($m=="within-file")
{
$input .="Association analysis
";
$input .="-->Single SNP analyses
";
$input .="---->Population based sample
";
$input .="------>Disease trait
";
$input .="-------->Stratified/clustered sample tests
";
$input .="---------->Within-cluster permutation
";
if ($p==2)
{
$input .="-------->With adaptive permutation
";
$output .= "" .$out.".assoc | ";
$output .= "Association results |
";
$output .= "" .$out.".assoc.perm | ";
$output .= "Adaptive permutation empirical p-values |
";
}
elseif ($p==3)
{
$input .="-------->With maxT permutation
";
$output .= "" .$out.".assoc | ";
$output .= "Association results |
";
$output .= "" .$out.".assoc.mperm | ";
$output .= "max(T) permutation empirical p-values |
";
}
}
if ($m=="mh")
{
$input .="Association analysis
";
$input .="-->Single SNP analyses
";
$input .="---->Population based sample
";
$input .="------>Disease trait
";
$input .="-------->Stratified/clustered sample tests
";
$input .="---------->Cochran-Mantel-Haenszel tests
";
$input .="------------>SNP-disease association conditional on cluster
";
$output .= "" .$out.".cmh | ";
$output .= "Cochran-Mantel-Haenszel test 1 |
";
}
if ($m=="mh2")
{
$input .="Association analysis
";
$input .="-->Single SNP analyses
";
$input .="---->Population based sample
";
$input .="------>Disease trait
";
$input .="-------->Stratified/clustered sample tests
";
$input .="---------->Cochran-Mantel-Haenszel tests
";
$input .="------------>SNP-cluster association conditional on disease
";
$output .= "" .$out.".cmh2 | ";
$output .= "Cochran-Mantel-Haenszel test 2 |
";
}
if ($m=="homog")
{
$input .="Association analysis
";
$input .="-->Single SNP analyses
";
$input .="---->Population based sample
";
$input .="------>Disease trait
";
$input .="-------->Stratified/clustered sample tests
";
$input .="---------->Homogeneity of odds ratio tests
";
$output .= "" .$out.".homog | ";
$output .= "Between strata homogeneity test |
";
}
if ($m=="t2")
{
$input .="Association analysis
";
$input .="-->Single SNP analyses
";
$input .="---->Population based sample
";
$input .="------>Disease trait
";
$input .="-------->Set based test
";
$input .="---------->Hotelling's T2 multilocus test
";
if ($p==1)
{
$input .="------------>Without permutation
";
$output .= "" .$out.".T2 | ";
$output .= "Hotelling's T(2) test results |
";
}
elseif ($p==2)
{
$input .="------------>With adaptive permutation
";
$output .= "" .$out.".T2 | ";
$output .= "Hotelling's T(2) test results |
";
$output .= "" .$out.".T2.perm | ";
$output .= "Empirical significance values |
";
}
elseif ($p==3)
{
$input .="------------>With maxT permutation
";
$output .= "" .$out.".T2 | ";
$output .= "Hotelling's T(2) test results |
";
$output .= "" .$out.".T2.mperm | ";
$output .= "Empirical significance values |
";
}
}
if ($m=="sumstat")
{
$input .="Association analysis
";
$input .="-->Single SNP analyses
";
$input .="---->Population based sample
";
$input .="------>Disease trait
";
$input .="-------->Set based test
";
$input .="---------->Sum-statistics gene-based test
";
$output .= "" .$out.".assoc.set | ";
$output .= "Sum-statistics set-based tests |
";
}
if ($m=="qt")
{
$input .="Association analysis
";
$input .="-->Single SNP analyses
";
$input .="---->Population based sample
";
$input .="------>Quantitative trait
";
if ($p==1)
{
$input .="-------->Without permutation
";
$output .= "" .$out.".qassoc | ";
$output .= "Quantitative trait association results |
";
$output .= "" .$out.".assoc | ";
$output .= "Association results |
";
}
elseif ($p==2)
{
$input .="-------->With adaptive permutation
";
$output .= "" .$out.".qassoc | ";
$output .= "Quantitative trait association results |
";
$output .= "" .$out.".assoc | ";
$output .= "Association results |
";
$output .= "" .$out.".assoc.perm | ";
$output .= "Adaptive permutation empirical p-values |
";
}
elseif ($p==3)
{
$input .="-------->With maxT permutation
";
$output .= "" .$out.".qassoc | ";
$output .= "Quantitative trait association results |
";
$output .= "" .$out.".assoc | ";
$output .= "Association results |
";
$output .= "" .$out.".assoc.mperm | ";
$output .= "max(T) permutation empirical p-values |
";
}
}
if ($m=="qt-within-file")
{
$input .="Association analysis
";
$input .="-->Single SNP analyses
";
$input .="---->Population based sample
";
$input .="------>Within-cluster permutation
";
if ($p==2)
{
$input .="-------->With adaptive permutation
";
$output .= "" .$out.".qassoc | ";
$output .= "Quantitative trait association results |
";
$output .= "" .$out.".assoc | ";
$output .= "Association results |
";
$output .= "" .$out.".assoc.perm | ";
$output .= "Adaptive permutation empirical p-values |
";
}
elseif ($p==3)
{
$input .="-------->With maxT permutation
";
$output .= "" .$out.".qassoc | ";
$output .= "Quantitative trait association results |
";
$output .= "" .$out.".assoc | ";
$output .= "Association results |
";
$output .= "" .$out.".assoc.mperm | ";
$output .= "max(T) permutation empirical p-values |
";
}
}
if ($m=="gxe")
{
$input .="Association analysis
";
$input .="-->Single SNP analyses
";
$input .="---->Population based sample
";
$input .="------>Quantitative trait GxE analysis
";
$output .= "" .$out.".qassoc.gxe | ";
$output .= "Quantitative GxE results |
";
}
// --- Association Analysis/Single SNP analyses/Family-based Sample -----------------
if ($m=="tdt")
{
$input .= "Association analysis
";
$input .= "-->Single SNP analyses
";
$input .= "---->Family-based sample
";
$input .= "------>Disease traits: TDT analysis
";
$output .= "" .$out.".tdt | ";
$output .= "TDT/parenTDT asymptotic results |
";
if ($p==2)
{
$output .= "" .$out.".tdt.perm | ";
$output .= "TDT/parenTDT adaptive permutaion results |
";
}
if ($p==3)
{
$output .= "" .$out.".tdt.mperm | ";
$output .= "TDT/parenTDT maxT permutaion results |
";
}
if ($set=="no") { $input .= "-------->Single SNP TDT only
";}
elseif ($set=="true") { $input .= "-------->Single SNP and set-based TDT
";}
}
if ($m=="qtdt")
{
$input .= "Association analysis
";
$input .= "-->Single SNP analyses
";
$input .= "---->Family-based sample
";
$input .= "------>Quantitative trait: gene-dropping permutation
";
$output .= "" .$out."[[]] | ";
$output .= " |
";
if ($p==1) {$input .= "-------->Gene-drop from founders
";}
if ($p==2) {$input .= "-------->Gene-drop from parents
";}
}
// ----- Epistatic Analysis -------------------------------------------------
if ($m=="epi")
{
$input .= "Association analysis
";
$input .= "-->Epistatic analyses
";
$input .= "---->SNP x SNP epistasis
";
if ($p==1)
{
$output .= "" .$out.".epi-co1 | ";
$output .= "Epistasis: case-only pairwise results |
";
$output .= "" .$out.".epi-co2 | ";
$output .= "Epistasis: case-only summary results |
";
}
elseif ($p==2)
{
$output .= "" .$out.".epi-cc1 | ";
$output .= "Epistasis: case/control pairwise results |
";
$output .= "" .$out.".epi-cc2 | ";
$output .= "Epistasis: case/control summary results |
";
}
}
if ($m=="genepi")
{
$input .= "Association analysis
";
$input .= "-->Epistatic analyses
";
$input .= "---->Gene-based epistasis
";
$output .= "" .$out.".genepi.dat | ";
$output .= " |
";
$output .= "" .$out.".genepi.R | ";
$output .= " |
";
}
if ($m=="epi" || $m=="genepi")
{
if ($p==1) {$input .= "------>Case-only analysis
";}
elseif ($p==2) {$input .= "------>Case/control analysis
";}
}
//_____End Association Analysis_________________________________________________________
?>