mkGenABELphenotype

Generate the .phe (PLINK phenotype) file needed by GenAbel. The person
 must match that specified in the .tfam file

internal

Uses as input genetic data that have been reformatted and
stored in a 'SQLite' database; this database is initially created
by the standalone 'mega2' C++ program (available freely from
<https://watson.hgen.pitt.edu/register/>). Loads and manipulates
data frames containing genotype, phenotype, and family
information from the input 'SQLite' database, and decompresses
needed subsets of the genotype data, on the fly, in a memory
efficient manner. We have also created several more functions
that illustrate how to use the data frames as well as perform
useful tasks: these permit one to run the 'pedgene' package to
carry out gene-based association tests on family data using
selected marker subsets, to run the 'SKAT' package to carry out
gene-based association tests using selected marker subsets, to
run the 'famSKATRC' package to carry out gene-based association
tests on families (optionally) and with rare or common variants
using selected marker subsets, to output the 'Mega2R' data as a
VCF file and related files (for phenotype and family data), and
to convert the data frames into CoreArray Genomic Data Structure
(GDS) format.

Daniel E Weeks

Mega2R

Accessing and Processing a 'Mega2' Genetic Database

 University of Pittsburgh

mkGenABELphenotype function

<dl><dt>envir</dt>
<dd>'environment' containing SQLite database and other globals</dd></dl>

Arguments

generate required PLINK (.phe) file — mkGenABELphenotype

<dl>

<dt>envir</dt>
<dd>'environment' containing SQLite database and other globals</dd>

</dl>

mkGenABELphenotype: generate required PLINK (.phe) file

Description

Usage

Value

Arguments

Examples