Mega2R package - RDocumentation

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Mega2R Bitbucket repository

Mega2R is an R package that makes it easy to load SQLite databases created by Mega2 directly into R as data frames. It also provides support for carrying out gene-based association tests, automatically looping over genes, using a variety of other R packages. For more information about Mega2R, see this web page: https://watson.hgen.pitt.edu/mega2/mega2r/

The latest development snapshot of the Mega2R R package can be obtained from this Bitbucket repository. Please note that this development snapshot is not as thoroughly tested as our stable release version, but does contain the newest features and changes.

To obtain the stable release version, please go to https://CRAN.R-project.org/package=Mega2R

Contact

Daniel E. Weeks, Ph.D.
Professor of Human Genetics and Biostatistics
Department of Human Genetics
University of Pittsburgh
Public Health 3119
130 DeSoto Street
Pittsburgh, PA 15261
USA

Work: 1 412 624 5388
Email: weeks@pitt.edu
Web site: https://watson.hgen.pitt.edu
Twitter: @StatGenDan

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Version

Install

install.packages('Mega2R')

Monthly Downloads

52

Version

1.0.5

License

GPL-2

Maintainer

Daniel E Weeks

Last Published

February 28th, 2019

Functions in Mega2R (1.0.5)

generate gwaa.data-class object from a Mega2R database

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

computeDosage function

Mega2GenABELClean

delete temporary PLINK tped files processed by GenABEL

read Mega2 SQLite database into R

generate the .ped, .fam and .map files of PLINK PED representation of a gwaa.data-class object

dump_mega2rtutorial_data

dump tutorial data

SKAT call back function

DofamSKATRC call back function

mk_unified_genotype_table

concatenate separate genotype vectors for each chromosome to one extended vector containing all the chromosomes and store it in the environment.

assemble pedigree information into a data frame

Mega2R-TBLSFilter

Mega2R SQLite3 table filter

set default range data: chromosome and start/end base pair

replace the pedigree data frame

generate required fam family for PLINK TPED (.tfam) file

execute the CRAN SKAT function on a subset of the gene transcripts

transcode mega2 to gdsfmt/SNP_ARRAY

Execute the pedgene function on a transcript ranges

generate a PLINK TPED file for GenABEL

generate required VCF frequency (.freq) file

getgenotypesdos

fetch dosage integer matrix for specified markers

pull allele pairs

getgenotypesgenabel

process the genotype matrix for specified markers and return the corresponding GenABEL genotype matrix

getgenotype_person

return the genotypes for all markers of a given person

load Mega2 SQLite database and perform initialization for famSKATRC usage

generate required VCF header

generate allele pairs in with MAJ(or) allele first

Mega2GenABELtst

compare two gwaa.data-class objects

mkGenABELcoding

generate GenABEL coding vector

load Mega2 SQLite database and perform initialization for pedgene usage

generate required PLINK (.phe) file

mk_markers_with_skip

make the derived "markers" data frame and store it in the environment.

show the association between index no and phenotype

create "markers" data frame

generate required VCF family (.fam) file

pedgene call back function

Mega2ENVGenABEL

generate gwaa.data-class object

uniqueFamMember

regenerate fam data frame with unique values in member column

Mega2R SQLite3 tables

return an initialized environment

generate a VCF file set for a collection of markers

set default name of transcription database and name of database mapping gene name to entrez gene id

execute the CRAN famSKAT_RC function on a subset of the gene transcripts

fetch genotype character matrix for specified markers

applyFnToRanges

apply a function to all the genotypes for markers found in several specified ranges

fetch genotype matrix for specified markers (assemble by rows)

getgenotypesraw

fetch genotype integer matrix for specified markers

clean_mega2rtutorial_data

remove tutorial data

load Mega2 SQLite database and perform initialization for SKAT usage

show the association between mapno and mapname

show Mega2R environment, viz. data frames and related info.

mkGenABELphenotype

generate required PLINK (.phe) file

mkGenABELgenotype

generate GenABEL compressed genotype matrix

where_mega2rtutorial_data

show directory of tutorial data

generate required Mega2 map (.map) file

generate required Mega2 penetrance (.pen) file

generate a phenotype data frame

load Mega2 database and initialize family data frame and markers data frame