Testing of SNPs and SNP Interactions in Case-Parent Trio Studies

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Documentation for package ‘trio’ version 3.43.0

• DESCRIPTION file.
• User guides, package vignettes and other documentation.

Help Pages

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.colGxEunstruct	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
qingEnv	Generate Trio Data Format Suitable for Trio Logic Regression
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