Package: Mega2R 1.1.0

Mega2R: Accessing and Processing a 'Mega2' Genetic Database

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.

Authors:Robert V. Baron [aut], Daniel E. Weeks [aut, cre], University of Pittsburgh [cph]

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Mega2R.pdf |Mega2R.html✨
Mega2R/json (API)
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38 exports 0.49 score 65 dependencies 1 mentions 8 scripts 349 downloads

Last updated 9 months agofrom:8446b75127. Checks:OK: 4 NOTE: 5. Indexed: yes.

Exports:applyFnToGenesapplyFnToMarkersapplyFnToRangesclean_mega2rtutorial_datacomputeDosagedbmega2_importDOfamSKATRCDOpedgeneDOSKATdump_mega2rtutorial_datagetgenotype_persongetgenotypesgetgenotypesdosgetgenotypesgenabelgetgenotypesrawinit_famSKATRCinit_pedgeneinit_SKATMega2ENVGenABELMega2famSKATRCMega2gdsfmtMega2GenABELMega2GenABELtstMega2pedgeneMega2SKATMega2VCFmkfammkMarkersmkphenotyperead.Mega2DBsetAnnotationssetfamsetRangesshowMapNamesshowMega2ENVshowPhenoNamesuniqueFamMemberwhere_mega2rtutorial_data

Dependencies:AnnotationDbiaskpassbdsmatrixBiobaseBiocGenericsBiostringsbitbit64blobcachemcliCompQuadFormcoxmecpp11crayoncurlDBIevaluatefamSKATRCfastmapgdsfmtGenomeInfoDbGenomeInfoDbDatagluehighrhttrIRangesjsonliteKEGGRESTkinship2knitrlatticelifecycleMatrixmemoisemimeminqamitoolsnlmenumDerivopensslpedgenepkgconfigplogrpngquadprogR6RcppRcppArmadilloRcppEigenrlangRSpectraRSQLiteS4VectorsSKATSPAtestsurveysurvivalsysUCSC.utilsvctrsxfunXVectoryamlzlibbioc