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trio (version 3.10.0)

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

Description

Testing SNPs and SNP interactions with a genotypic TDT. This package furthermore contains functions for computing pairwise values of LD measures and for identifying LD blocks, as well as functions for setting up matched case pseudo-control genotype data for case-parent trios in order to run trio logic regression, for imputing missing genotypes in trios, for simulating case-parent trios with disease risk dependent on SNP interaction, and for power and sample size calculation in trio data.

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Version

Monthly Downloads

125

Version

3.10.0

License

LGPL-2

Maintainer

Holger Schwender

Last Published

February 15th, 2017

Functions in trio (3.10.0)

Computation of LD Measures

SAM and EBAM for Trio Data

Genotypic TDT for Gene-Environment Interactions

Generates Case-Pseudo-Control Matrix

Permutation-Based gTDT for Two-Way Interactions

EM Likelihood Ratio Test

Parent-of-Origin Tests

Identifying LD blocks

Maximum Genotypic TDT

Printing of trioLR Objects

Plotting for trioLR Objects

TDT on genotype probabilities matrix

Roots of a Fourth Degree Polynomial

Printing and plotting of a trioFS object

Printing and Storing of colGxE objects

Plotting a LDblock Object

Plotting a getLD or getLDlarge Object

Control Parameters for Trio Logic Regression

Transformation of Ped-File

Trio Logic Regression

Reading a Ped File

Transformation of VFC File

Score Tests for SNPs, GxE, and GxG Interactions

Case-Parent Trio Data

Remove SNPs or Trios

Permutation Tests for Trio Logic Regression

Simulate Case-Parent Trios

Trio Feature Selection

Check Case-Parent Trio Data for Mendelian Errors

Genotypic TDT for Two-Way Interactions

Generate Trio Data Format Suitable for Trio Logic Regression

Power and sample size calculation