Man pages for GenABEL
genome-wide SNP association analysis
| add.phdata | Adds phenotypic variables to gwaa.data object |
| add.plot | function to plot additional GWAA results |
| arrange_probabel_phe | arranges ProbABEL phenotype-file |
| as.character.gwaa.data | Attempts to convert genotypic part of gwaa.data to character |
| as.character.snp.coding | Attempts to convert internal snp.coding-class to character |
| as.character.snp.data | Attempts to convert snp.data to character |
| as.character.snp.strand | Attempts to convert internal strand-class to character |
| as.data.frame.gwaa.data | Attempts to convert snp.data to "hsgeno" |
| as.double.gwaa.data | Attempts to convert gwaa.data to double |
| as.double.snp.data | Attempts to convert snp.data to double |
| as.genotype | Attempts to convert object to "genotype" |
| as.genotype.gwaa.data | Attempts to convert gwaa.data to "genotype" |
| as.genotype.snp.data | Attempts to convert snp.data to "genotype" |
| as.hsgeno | Attempts to convert object to "hsgeno" |
| as.hsgeno.gwaa.data | Attempts to convert gwaa.data to "hsgeno" |
| as.hsgeno.snp.data | Attempts to convert snp.data to "hsgeno" |
| autosomal | Function telling all autosomal SNPs |
| blurGenotype | blur genotype calls into probabilites |
| catable | function to generate summary table for quantitative data |
| ccfast | fast case-control analysis |
| check.marker | function to do genotypic quality control |
| check.marker-class | Class "check.marker" |
| checkPackageVersionOnCRAN | checks what is the version of package on CRAN |
| check.trait | function to do primitive trait quality control |
| cocohet | Test for compound heterozygote effects |
| convert.snp.affymetrix | function to convert genotypic data from Affymetrix to... |
| convert.snp.illumina | function to convert genotypic data from Illumina/Affymetrix... |
| convert.snp.mach | function to convert genotypic data from MACH format to... |
| convert.snp.ped | function to convert genotypic data in pedigree fromat (+map)... |
| convert.snp.text | function to convert integer genotypic data file to raw... |
| convert.snp.tped | function to convert genotypic data in transposed-ped format... |
| crnames | Return column and row names |
| del.phdata | delete phenotypes from phdata |
| descriptives.marker | Function to generate descriptive summary tables for genotypic... |
| descriptives.scan | Function to describe "top" hits in GWA scan |
| descriptives.trait | Function to generate descriptive summary tables for... |
| dprfast | Estimates D' between multiple markers |
| egscore | Fast score test for association, corrected with PC |
| egscore.old | Fast score test for association, corrected with PC |
| emp.ccfast | Genome-wide significance for a case-control GWA scan |
| emp.qtscore | Genome-wide significance for a GWA scan |
| estlambda | Estimate the inflation factor for a distribution of P-values |
| export.impute | function to export GenABEL data in IMPUTE format |
| export.merlin | function to export GenABEL data in merlin format |
| export.plink | Export GenABEL data in PLINK format |
| extract.annotation.impute | extracts SNP annotation from IMPUTE files |
| extract.annotation.mach | extracts SNP annotation from MACH/HapMap legend files |
| findRelatives | guesses relations between individuals |
| formetascore | function to run GWA analysis oriented for future... |
| GASurv | Makes survival data object for reg.gwaa |
| GenABEL | GWAS in R |
| generateOffspring | simulates offspring's genotypes |
| getLogLikelihoodGivenRelation | computes logLik of two blurGenotypes |
| grammar | GRAMMAR test for association in samples with genetic... |
| gwaa.data-class | Class "gwaa.data" |
| hom | function to compute average homozygosity within a person |
| hom.old | function to compute average homozygosity within a person |
| HWE.show | show HWE tables |
| ibs | Computes (average) Idenity-by-State for a set of people and... |
| ibs.old | Computes (average) Idenity-by-State for a set of people and... |
| impute2databel | converts IMPUTE-imputed files to DatABEL (filevector) format |
| impute2mach | converts IMPUTE to MACH files |
| load.gwaa.data | function to load GWAA data |
| mach2databel | converts MACH-imputed files to DatABEL (filevector) format |
| makeTransitionMatrix | Genotype transition probabilities matrices |
| merge.gwaa.data | function to merge objects of gwaa.data-class |
| merge.snp.data | function to merge objects of snp.data-class |
| mlreg | Linear and logistic regression and Cox models for genome-wide... |
| mlreg.p | EXPERIMENTAL Linear and logistic regression and Cox models... |
| mmscore | Score test for association in related people |
| npsubtreated | non-parametric trait "imputations" in treated people |
| patch_strand | function to change strand |
| perid.summary | Summary of marker data per person |
| PGC | Polynomial genomic control |
| plot.check.marker | plots "check.marker" object |
| plot.scan.gwaa | function to plot GWAA results |
| plot.scan.gwaa.2D | function to plot 2D scan results |
| polygenic | Estimation of polygenic model |
| polygenic_hglm | Estimation of polygenic model |
| qtscore | Fast score test for association |
| qvaluebh95 | Computes Benjamini-Hochberg (95) q-value |
| r2fast | Estimates r2 between multiple markers |
| r2fast.old | Estimates r2 between multiple markers |
| recodeChromosome | Change chromosomal coding |
| reconstructNPs | reconstruct nuclear families |
| redundant | function to do redundancy check |
| refresh.gwaa.data | Updates an object from old to new GenABEL format |
| rhofast | Estimates rho between multiple markers |
| rntransform | Rank-transformation to normality |
| save.gwaa.data | function to save gwaa.data object |
| scan.glm | Scan GWA data using glm |
| scan.glm.2D | Scans regional data allowing for gene-gene interaction using... |
| scan.gwaa.2D-class | Class "scan.gwaa.2D" |
| scan.gwaa-class | Class "scan.gwaa" |
| scan.haplo | scan.haplo |
| scan.haplo.2D | runs haplo.score.slide with all pairs of markers in a region |
| show.ncbi | Shows the region on NCBI map |
| snp.coding-class | Class "snp.coding" |
| snp.data | creates an snp.data object |
| snp.data-class | Class "snp.data" |
| snp.mx-class | Class "snp.mx" |
| snp.names | extracts names of SNPs in a region |
| snps.cell-class | Class "snps.cell" |
| snp.strand-class | Class "snp.strand" |
| snp.subset | function to subset objects of class scan.gwaa and... |
| sortmap.internal | Internal function for map-sorting |
| sset | Internal use function for class snp.mx-class |
| summary.check.marker | Summary of check.marker object |
| summary.gwaa.data | function to summarise GWAA data |
| summary.scan.gwaa | Shortcut to 'descriptives... |
| summary.snp.data | function to summary GWAA data |
| VIFGC | Genomic control for various model of inheritance using VIF |
| VIFGC_ovdom | Genomic control for over-dominant model of inheritance using... |
| Xfix | function to set impossible genotypes as missing |
| ztransform | Transformation to standard Normal |
