Detection of disease-associated SNP interactions in case-parent trio data


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Documentation for package ‘trio’ version 1.2.9

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colGxE Genotypic TDT for Gene-Environment Interactions
colGxEPerms Genotypic TDT for Gene-Environment Interactions
colMAFtrio Remove SNPs or Trios
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
getLD Computation of LD Measures
gtdt.ebam SAM and EBAM for Trio Data
gtdt.stat SAM and EBAM for Trio Data
LDdata Case-Parent Trio Data
mat Computation of LD Measures
mat.test Case-Parent Trio Data
orderSNPs Remove SNPs or Trios
ped2geno Transformation of Ped-File
plot.getLD Plotting a getLD Object
plot.LDblocks Plotting a LDblock Object
poly4root Roots of a Fourth Degree Polynomial
poly4rootMat Roots of a Fourth Degree Polynomial
print.colGxE Genotypic TDT for Gene-Environment Interactions
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.scoreGxE Score Tests for SNPs, GxE, and GxG Interactions
print.scoreTDT Score Tests for SNPs, GxE, and GxG Interactions
print.tdt Genotypic TDT
print.tdtEpi Genotypic TDT for Two-Way Interactions
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
trio Generate Trio Data Format Suitable for Trio Logic Regression
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.sim Simulate Case-Parent Trios