init_SKAT

This populates the R data frames from the specified Mega2 SQLite database. It then
 prunes the samples to only include members that have a definite case or control
 status. Undefined samples are ignored.

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

init_SKAT function

<dl><dt>db</dt>
<dd>specifies the path of a Mega2 SQLite database containing study data.</dd>
<dt>verbose</dt>
<dd>TRUE indicates that diagnostic printouts should be enabled.
This value is saved in the returned environment.</dd>
<dt>allMarkers</dt>
<dd>TRUE means use all markers in a given transcript even if there is no
variation. FALSE means ignore markers that show no variation; this is the default.</dd>
<dt>...</dt>
<dd>fed to dbmega2_import(); should be bpPosMap= to select from the maps of
base pairs, if the default is not desired.</dd></dl>

Arguments

load Mega2 SQLite database and perform initialization for SKAT usage — init_SKAT

<dl>

<dt>db</dt>
<dd>specifies the path of a Mega2 SQLite database containing study data.</dd>


<dt>verbose</dt>
<dd>TRUE indicates that diagnostic printouts should be enabled.
This value is saved in the returned environment.</dd>


<dt>allMarkers</dt>
<dd>TRUE means use all markers in a given transcript even if there is no
variation. FALSE means ignore markers that show no variation; this is the default.</dd>


<dt>...</dt>
<dd>fed to dbmega2_import(); should be bpPosMap= to select from the maps of
base pairs, if the default is not desired.</dd>

</dl>

init_SKAT: load Mega2 SQLite database and perform initialization for SKAT usage

Description

Usage

Value

Arguments

See Also

Examples