# Accessing and Processing a 'Mega2' Genetic Database

## Documentation for package ‘Mega2R’ version 1.1.0

- DESCRIPTION file.
- User guides, package vignettes and other documentation.
- Package NEWS.

## Help Pages

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
DOfamSKATRC | DofamSKATRC call back function
DOpedgene | pedgene call back function
DOSKAT | SKAT call back function
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_famSKATRC | load Mega2 SQLite database and perform initialization for famSKATRC usage
init_pedgene | load Mega2 SQLite database and perform initialization for pedgene usage
init_SKAT | load Mega2 SQLite database and perform initialization for SKAT usage
Mega2ENVGenABEL | generate gwaa.data-class object
Mega2famSKATRC | execute the CRAN famSKAT_RC function on a subset of the gene transcripts
Mega2gdsfmt | transcode mega2 to gdsfmt/SNP_ARRAY
Mega2GenABEL | generate gwaa.data-class object from a *Mega2R* database
Mega2GenABELtst | compare two gwaa.data-class objects
Mega2pedgene | Execute the pedgene function on a transcript ranges
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
mkfam | assemble pedigree information into a data frame
mkMarkers | create "markers" 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
setfam | replace the pedigree data frame
setRanges | set default range data: chromosome and start/end base pair
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
TBLS | Mega2R SQLite3 tables
TBLSFilter | Mega2R SQLite3 table filter
uniqueFamMember | regenerate fam data frame with unique values in member column
where_mega2rtutorial_data | show directory of tutorial data