Accessing and Processing a 'Mega2' Genetic Database
apply a function to the genotypes (markers) in each gene transcript an...
apply a function to the genotypes from a set of markers
apply a function to all the genotypes for markers found in several spe...
remove tutorial data
computeDosage function
read Mega2 SQLite database into R
generate the .ped, .fam and .map files of PLINK PED representation of ...
DofamSKATRC call back function
pedgene call back function
SKAT call back function
dump tutorial data
pull allele pairs
return the genotypes for all markers of a given person
fetch genotype character matrix for specified markers
fetch genotype matrix for specified markers (assemble by rows)
fetch dosage integer matrix for specified markers
process the genotype matrix for specified markers and return the corre...
fetch genotype integer matrix for specified markers
load Mega2 SQLite database and perform initialization for famSKATRC us...
load Mega2 SQLite database and perform initialization for pedgene usag...
load Mega2 SQLite database and perform initialization for SKAT usage
generate gwaa.data-class object
execute the CRAN famSKAT_RC function on a subset of the gene transcrip...
transcode mega2 to gdsfmt/SNP_ARRAY
generate gwaa.data-class object from a Mega2R database
delete temporary PLINK tped files processed by GenABEL
compare two gwaa.data-class objects
Execute the pedgene function on a transcript ranges
Mega2R: Accessing and Processing a 'Mega2' Genetic Database
Mega2R SQLite3 tables
Mega2R SQLite3 table filter
Mega2R version
execute the CRAN SKAT function on a subset of the gene transcripts
generate a VCF file set for a collection of markers
make the derived "markers" data frame and store it in the environment.
concatenate separate genotype vectors for each chromosome to one exten...
generate allele pairs in with MAJ(or) allele first
assemble pedigree information into a data frame
generate GenABEL coding vector
generate GenABEL compressed genotype matrix
generate required PLINK (.phe) file
generate required fam family for PLINK TPED (.tfam) file
generate a PLINK TPED file for GenABEL
create "markers" data frame
generate a phenotype data frame
generate required VCF family (.fam) file
generate required VCF frequency (.freq) file
generate required VCF header
generate required Mega2 map (.map) file
generate required Mega2 penetrance (.pen) file
generate required PLINK (.phe) file
load Mega2 database and initialize family data frame and markers data ...
return an initialized environment
set default name of transcription database and name of database mappin...
replace the pedigree data frame
set default range data: chromosome and start/end base pair
show the association between mapno and mapname
show Mega2R environment, viz. data frames and related info.
show the association between index no and phenotype
regenerate fam data frame with unique values in member column
show directory of tutorial data
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.
Useful links