Mega2GenABELcoding

data frame of markers to be processed

markers

frequency of first allele calculated from actual data. The Mega2 internal frequencies may be
a bit stale. This value is one of two returned by the *Mega2GenABELconvert()* function.

Freq.x

'environment' containing SQLite database and other globals

envir

Each element of the coding vector is the index of the corresponding genotype in the GenABEL:::alleleID.codes() array.
 The genotypes are ordered so the allele with the greater frequency appears first.

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 output the
'Mega2R' data as a VCF file and related files (for phenotype and
family data), and to convert the data frames into 'GenABEL'
gwaa.data-class objects.

Mega2GenABELcoding: generate GenABEL coding vector

Description

Usage

Arguments

Value

Examples