mkVCFfreq

prefix

data.frame of markers being processed

markers

use 1/2 instead of two given alleles (eg. A/C)

recode

"environment" containing SQLite database and other globals

envir

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 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.

mkVCFfreq: generate required VCF frequency (.freq) file

Description

Usage

Arguments

Value

Examples