setfam

You should first modify the fam data frame to filter the members you need to remove.
 (For example, you might want to delete members that have an unknown case/control status.)
 This function takes a new data frame of pedigree information and replaces the fam
 data frame in the 'environment' with it. Additionally,
 changing fam data frame will filter the genotypes data frame to only contain persons
 matching those in the fam data frame. <code>setfam</code> also filters for the phenotype data
 records.

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

setfam function

<dl><dt>fam</dt>
<dd>data frame of family information filtered from fam
data frame (generated by <code>mkfam</code>).</dd>
<dt>envir</dt>
<dd>an 'environment' that contains all the data frames created from the SQLite database.</dd></dl>

Arguments

replace the pedigree data frame — setfam

<dl>

<dt>fam</dt>
<dd>data frame of family information filtered from fam
data frame (generated by <code>mkfam</code>).</dd>


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

</dl>

setfam: replace the pedigree data frame

Description

Usage

Value

Arguments

Examples