allelicTDT |
Allelic TDT |
colEMlrt |
EM Likelihood Ratio Test |
colGxE |
Genotypic TDT for Gene-Environment Interactions |
colGxEPerms |
Genotypic TDT for Gene-Environment Interactions |
colGxG |
Genotypic TDT for Two-Way Interactions |
colGxGPerms |
Permutation-Based gTDT for Two-Way Interactions |
colMAFtrio |
Remove SNPs or Trios |
colPOlrt |
Parent-of-Origin Tests |
colTAT |
Parent-of-Origin Tests |
colTDT |
Genotypic TDT |
colTDT2way |
Genotypic TDT for Two-Way Interactions |
colTDTebam |
SAM and EBAM for Trio Data |
colTDTinter2way |
Genotypic TDT for Two-Way Interactions |
colTDTmaxStat |
Maximum Genotypic TDT |
colTDTmaxTest |
Maximum Genotypic TDT |
colTDTsam |
SAM and EBAM for Trio Data |
compPermTDT2way |
Permutation-Based gTDT for Two-Way Interactions |
fastGxG |
Genotypic TDT for Two-Way Interactions |
fastGxGrec |
Genotypic TDT for Two-Way Interactions |
findLDblocks |
Identifying LD blocks |
freq.hap |
Case-Parent Trio Data |
getGxEstats |
Printing and Storing of colGxE objects |
getLD |
Computation of LD Measures |
getLDlarge |
Computation of LD Measures |
getMatPseudo |
Generates Case-Pseudo-Control Matrix |
gtdt.ebam |
SAM and EBAM for Trio Data |
gtdt.stat |
SAM and EBAM for Trio Data |
LDdata |
Case-Parent Trio Data |
lrControl |
Control Parameters for Trio Logic Regression |
mat.test |
Case-Parent Trio Data |
orderSNPs |
Remove SNPs or Trios |
ped2geno |
Transformation of Ped-File |
plot.getLD |
Plotting a getLD or getLDlarge Object |
plot.getLDlarge |
Plotting a getLD or getLDlarge Object |
plot.LDblocks |
Plotting a LDblock Object |
plot.trioFS |
Printing and plotting of a trioFS object |
plot.trioLR |
Plotting for trioLR Objects |
poly4root |
Roots of a Fourth Degree Polynomial |
poly4rootMat |
Roots of a Fourth Degree Polynomial |
print.aTDT |
Allelic TDT |
print.colEMlrt |
EM Likelihood Ratio Test |
print.colGxE |
Printing and Storing of colGxE objects |
print.colTDT |
Genotypic TDT |
print.colTDTepi |
Genotypic TDT for Two-Way Interactions |
print.LDblock |
Identifying LD blocks |
print.maxScoreTrio |
Score Tests for SNPs, GxE, and GxG Interactions |
print.maxStatTrio |
Maximum Genotypic TDT |
print.maxTestTrio |
Maximum Genotypic TDT |
print.polrt |
Parent-of-Origin Tests |
print.scoreGxE |
Score Tests for SNPs, GxE, and GxG Interactions |
print.scoreTDT |
Score Tests for SNPs, GxE, and GxG Interactions |
print.tat |
Parent-of-Origin Tests |
print.tdt |
Genotypic TDT |
print.tdtEpi |
Genotypic TDT for Two-Way Interactions |
print.trio.power |
Power and sample size calculation |
print.trioFS |
Printing and plotting of a trioFS object |
print.trioLR |
Printing of trioLR Objects |
prob.mat.test |
Case-Parent Trio Data |
probTDT |
TDT on genotype probabilities matrix |
read.pedfile |
Reading a Ped File |
removeSNPs |
Remove SNPs or Trios |
removeTrios |
Remove SNPs or Trios |
scoreGxE |
Score Tests for SNPs, GxE, and GxG Interactions |
scoreGxG |
Score Tests for SNPs, GxE, and GxG Interactions |
scoreMaxStat |
Score Tests for SNPs, GxE, and GxG Interactions |
scoreTDT |
Score Tests for SNPs, GxE, and GxG Interactions |
simuBkMap |
Case-Parent Trio Data |
splitBlocks |
Identifying LD blocks |
step3way |
Case-Parent Trio Data |
tdt |
Genotypic TDT |
tdt2way |
Genotypic TDT for Two-Way Interactions |
tdtGxG |
Genotypic TDT for Two-Way Interactions |
trio.check |
Check Case-Parent Trio Data for Mendelian Errors |
trio.data |
Case-Parent Trio Data |
trio.gen.err |
Case-Parent Trio Data |
trio.gen1 |
Case-Parent Trio Data |
trio.gen2 |
Case-Parent Trio Data |
trio.ped.err |
Case-Parent Trio Data |
trio.ped1 |
Case-Parent Trio Data |
trio.ped2 |
Case-Parent Trio Data |
trio.permTest |
Permutation Tests for Trio Logic Regression |
trio.power |
Power and sample size calculation |
trio.prepare |
Generate Trio Data Format Suitable for Trio Logic Regression |
trio.sim |
Simulate Case-Parent Trios |
trioFS |
Trio Feature Selection |
trioFS.default |
Trio Feature Selection |
trioFS.formula |
Trio Feature Selection |
trioFS.trioPrepare |
Trio Feature Selection |
trioLR |
Trio Logic Regression |
trioLR.default |
Trio Logic Regression |
trioLR.formula |
Trio Logic Regression |
trioLR.trioPrepare |
Trio Logic Regression |
vcf2geno |
Transformation of VFC File |