setAnnotations

This function takes two string parameters:
 one to specify entrez gene ids to transcripts,
 the other to map gene names to entrez gene id's.

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

setAnnotations function

<dl><dt>txdb</dt>
<dd>name of Bioconductor transcription database.</dd>
<dt>entrezGene</dt>
<dd>name of Bioconductor mapping of gene name or gene alias to entrez gene id</dd>
<dt>envir</dt>
<dd>an 'environment' that contains all the data frames created from the SQLite database.</dd></dl>

Arguments

set default name of transcription database and name of database mapping gene name to entrez gene id — setAnnotations

<dl>

<dt>txdb</dt>
<dd>name of Bioconductor transcription database.</dd>


<dt>entrezGene</dt>
<dd>name of Bioconductor mapping of gene name or gene alias to entrez gene id</dd>


<dt>envir</dt>
<dd>an 'environment' that contains all the data frames created from the SQLite database.</dd>

</dl>

setAnnotations: set default name of transcription database and name of database mapping gene name to entrez gene id

Description

Usage

Value

Arguments

Examples