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| GenABEL-package | GenABEL: an R package for Genome Wide Association Analysis |
| add.plot | function to plot additional GWAA results |
| as.character.gwaa.data | Attempts to convert genotypic part of gwaa.data to character |
| as.character.snp.data | Attempts to convert snp.data 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" |
| 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" |
| check.trait | function to do primitive trait quality control |
| coerce,snp.data,character-method | Class "snp.data" |
| coerce,snp.data,genotype-method | Class "snp.data" |
| coerce,snp.data,hsgeno-method | Class "snp.data" |
| coerce,snp.data,numeric-method | Class "snp.data" |
| coerce,snp.mx,character-method | Class "snp.mx" |
| coerce,snp.mx,numeric-method | Class "snp.mx" |
| convert.snp.ped | function to convert genotypic data in pre-makeped linkage fromat (+map) to internal genotypic data formated file |
| convert.snp.text | function to convert integer genotypic data file to raw internal data formated file |
| descriptives.marker | Function to generate descriptive summary tables for genotypic data |
| descriptives.scan | Function to describe "top" hits in GWA scan |
| descriptives.trait | Function to generate descriptive summary tables for phenotypic data |
| 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 |
| ge03d2 | GWA-type data on small region |
| ge03d2c | GWA-type data on small region |
| ge03d2ex | GWA-type data on small region |
| GenABEL | GenABEL: an R package for Genome Wide Association Analysis |
| gwaa.data-class | Class "gwaa.data" |
| hom | 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 markers |
| load.gwaa.data | function to load GWAA data |
| perid.summary | Summary of marker data per person |
| plot, check.marker-method | Class "check.marker" |
| plot, scan.gwaa-method | Class "scan.gwaa" |
| plot, scan.gwaa.2D-method | Class "scan.gwaa.2D" |
| 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 |
| qtscore | Fast score test for association |
| qvaluebh95 | Computes Benjamini-Hochberg (95) q-value |
| redundant | function to do redundancy check |
| 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 glm |
| scan.gwaa-class | Class "scan.gwaa" |
| scan.gwaa.2D-class | Class "scan.gwaa.2D" |
| scan.haplo | scan.haplo |
| scan.haplo.2D | runs haplo.score.slide with all pairs of markers in a region |
| show,gwaa.data-method | Class "gwaa.data" |
| show,snp.data-method | Class "snp.data" |
| show,snp.mx-method | Class "snp.mx" |
| show.ncbi | Shows the region on NCBI map |
| 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 |
| snp.subset | function to subset objects of class scan.gwaa and check.marker |
| snps.cell-class | Class "snps.cell" |
| srdta | GWA-type data on small region |
| sset | Internal use function for class snp.mx-class |
| summary, check.marker-method | Class "check.marker" |
| summary,gwaa.data-method | Class "gwaa.data" |
| summary,snp.data-method | Class "snp.data" |
| summary,snp.mx-method | Class "snp.mx" |
| summary.check.marker | Summary of check.marker object |
| summary.gwaa.data | function to summarise GWAA data |
| summary.snp.data | function to summary GWAA data |
| Xfix | function to set heterozygous male X-linked genotypes to NA |
| [,gwaa.data-method | Class "gwaa.data" |
| [,snp.data-method | Class "snp.data" |
| [,snp.mx-method | Class "snp.mx" |