DOSKAT                  SKAT call back function
DOfamSKATRC             DofamSKATRC call back function
DOpedgene               pedgene call back function
Mega2ENVGenABEL         generate gwaa.data-class object
Mega2GenABEL            generate gwaa.data-class object from a *Mega2R*
                        database
Mega2GenABELtst         compare two gwaa.data-class objects
Mega2R-TBLS             Mega2R SQLite3 tables
Mega2R-TBLSFilter       Mega2R SQLite3 table filter
Mega2RVersion           Mega2R version
Mega2SKAT               execute the CRAN SKAT function on a subset of
                        the gene transcripts
Mega2VCF                generate a VCF file set for a collection of
                        markers
Mega2famSKATRC          execute the CRAN famSKAT_RC function on a
                        subset of the gene transcripts
Mega2gdsfmt             transcode mega2 to gdsfmt/SNP_ARRAY
Mega2pedgene            Execute the pedgene function on a transcript
                        ranges
applyFnToGenes          apply a function to the genotypes (markers) in
                        each gene transcript and/or base pair range
applyFnToMarkers        apply a function to the genotypes from a set of
                        markers
applyFnToRanges         apply a function to all the genotypes for
                        markers found in several specified ranges
clean_mega2rtutorial_data
                        remove tutorial data
computeDosage           computeDosage function
dbmega2_import          read Mega2 SQLite database into R
dump_mega2rtutorial_data
                        dump tutorial data
getgenotypes            fetch genotype character matrix for specified
                        markers
getgenotypesdos         fetch dosage integer matrix for specified
                        markers
getgenotypesgenabel     process the genotype matrix for specified
                        markers and return the corresponding GenABEL
                        genotype matrix
getgenotypesraw         fetch genotype integer matrix for specified
                        markers
init_SKAT               load Mega2 SQLite database and perform
                        initialization for SKAT usage
init_famSKATRC          load Mega2 SQLite database and perform
                        initialization for famSKATRC usage
init_pedgene            load Mega2 SQLite database and perform
                        initialization for pedgene usage
mkMarkers               create "markers" data frame
mkfam                   assemble pedigree information into a data frame
mkphenotype             generate a phenotype data frame
read.Mega2DB            load Mega2 database and initialize family data
                        frame and markers data frame
setAnnotations          set default name of transcription database and
                        name of database mapping gene name to entrez
                        gene id
setRanges               set default range data: chromosome and
                        start/end base pair
setfam                  replace the pedigree data frame
showMapNames            show the association between mapno and mapname
showMega2ENV            show Mega2R environment, viz. data frames and
                        related info.
showPhenoNames          show the association between index no and
                        phenotype
uniqueFamMember         regenerate fam data frame with unique values in
                        member column
where_mega2rtutorial_data
                        show directory of tutorial data
