Man pages for Mega2R
Accessing and Processing a 'Mega2' Genetic Database
| applyFnToGenes | apply a function to the genotypes (markers) in each gene... |
| applyFnToMarkers | apply a function to the genotypes from a set of markers |
| applyFnToRanges | apply a function to all the genotypes for markers found in... |
| clean_mega2rtutorial_data | remove tutorial data |
| computeDosage | computeDosage function |
| dbmega2_import | read Mega2 SQLite database into R |
| dmpPed | generate the .ped, .fam and .map files of PLINK PED... |
| DOfamSKATRC | DofamSKATRC call back function |
| DOpedgene | pedgene call back function |
| DOSKAT | SKAT call back function |
| dump_mega2rtutorial_data | dump tutorial data |
| getAlleles | pull allele pairs |
| getgenotype_person | return the genotypes for all markers of a given person |
| 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... |
| getgenotypes_R | fetch genotype matrix for specified markers (assemble by... |
| getgenotypesraw | fetch genotype integer matrix for specified markers |
| init_famSKATRC | load Mega2 SQLite database and perform initialization for... |
| init_pedgene | load Mega2 SQLite database and perform initialization for... |
| init_SKAT | load Mega2 SQLite database and perform initialization for... |
| Mega2ENVGenABEL | generate gwaa.data-class object |
| Mega2famSKATRC | execute the CRAN famSKAT_RC function on a subset of the gene... |
| Mega2gdsfmt | transcode mega2 to gdsfmt/SNP_ARRAY |
| Mega2GenABEL | generate gwaa.data-class object from a *Mega2R* database |
| Mega2GenABELClean | delete temporary PLINK tped files processed by GenABEL |
| Mega2GenABELtst | compare two gwaa.data-class objects |
| Mega2pedgene | Execute the pedgene function on a transcript ranges |
| Mega2R-package | Mega2R: Accessing and Processing a 'Mega2' Genetic Database |
| 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... |
| Mega2VCF | generate a VCF file set for a collection of markers |
| mkAlleles | generate allele pairs in with MAJ(or) allele first |
| mkfam | assemble pedigree information into a data frame |
| mkGenABELcoding | generate GenABEL coding vector |
| mkGenABELgenotype | generate GenABEL compressed genotype matrix |
| mkGenABELphenotype | generate required PLINK (.phe) file |
| mkGenABELtfam | generate required fam family for PLINK TPED (.tfam) file |
| mkGenABELtped | generate a PLINK TPED file for GenABEL |
| mkMarkers | create "markers" data frame |
| mk_markers_with_skip | make the derived "markers" data frame and store it in the... |
| mkphenotype | generate a phenotype data frame |
| mk_unified_genotype_table | concatenate separate genotype vectors for each chromosome to... |
| mkVCFfam | generate required VCF family (.fam) file |
| mkVCFfreq | generate required VCF frequency (.freq) file |
| mkVCFhdr | generate required VCF header |
| mkVCFmap | generate required Mega2 map (.map) file |
| mkVCFpen | generate required Mega2 penetrance (.pen) file |
| mkVCFphe | generate required PLINK (.phe) file |
| read.Mega2DB | load Mega2 database and initialize family data frame and... |
| resetMega2ENV | return an initialized environment |
| setAnnotations | set default name of transcription database and name of... |
| 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 |
| uniqueFamMember | regenerate fam data frame with unique values in member column |
| where_mega2rtutorial_data | show directory of tutorial data |
