mkVCFfreq

Generate the initial boiler plate VCF, then generate ##INFO entries for each entry tag.
 Finally, generate the ##contig entries for each chromosome.

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

mkVCFfreq function

<dl><dt>prefix</dt>
<dd>prefix for .freq file (frequency)</dd>
<dt>markers</dt>
<dd>data.frame of markers being processed</dd>
<dt>recode</dt>
<dd>use 1/2 instead of two given alleles (eg. A/C)</dd>
<dt>envir</dt>
<dd>"environment" containing SQLite database and other globals</dd></dl>

Arguments

generate required VCF frequency (.freq) file — mkVCFfreq

<dl>

<dt>prefix</dt>
<dd>prefix for .freq file (frequency)</dd>


<dt>markers</dt>
<dd>data.frame of markers being processed</dd>


<dt>recode</dt>
<dd>use 1/2 instead of two given alleles (eg. A/C)</dd>


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

</dl>

mkVCFfreq: generate required VCF frequency (.freq) file

Description

Usage

Value

Arguments

Examples