R: Class "gwaa.data"

gwaa.data-class {GenABEL} | R Documentation

## Class "gwaa.data"

### Description

This class contains objects holding all GWAA data – phenotypes, genotypes and other relevant information

### Slots

`phdata`:

  dataframe with phenotypic data used in GWAA

`gtdata`:

  object of class `snp.data-class` used to store genotypic data, map, etc.

### Methods

[

  `signature(x = "gwaa.data", i = "ANY", j = "ANY", drop = "ANY")`: subset operations. x[i,j] will select people listed in i and SNPs listed in j.

show

  `signature(object = "gwaa.data")`: shows both parts of the object. Take care that the objects are usually very large!

summary

  `signature(object = "gwaa.data")`: Calls standard summary to describe phenotypic part and calls `summary.snp.data` to `snp.data-class`

gtdata

  `signature(object = "gwaa.data")`: returns genotypic data (object of `snp.data-class`)

phdata

  `signature(object = "gwaa.data")`: returns phenotypic data (a `data.frame`)

phdata<-

  `signature(object = "gwaa.data")`: method do modify phenotypic data (a `data.frame`)

### Author(s)

Yurii Aulchenko

### See Also

`snp.data-class`, `load.gwaa.data`, `snp.mx-class`

### Examples

    require(GenABEL.data)
    data(srdta)
    srdta@phdata[1:10,]
    srdta@gtdata[1:10,1:12]
    srdta[1:10,1:12]
    as.numeric(srdta@gtdata[1:12,1:10])
    # very long output:
    summary(srdta)

[Package GenABEL version 1.8-0 Index]