R: Class "scan.gwaa.2D"

scan.gwaa.2D-class {GenABEL} | R Documentation

## Class "scan.gwaa.2D"

### Description

This class contains results of 2D analysis. This is an list object, generated by `scan.glm.2D` or `scan.haplo.2D`.

### Names

snpnames

  list of names of SNPs tested

P1df

  corresponding list of P-values of allelic test for association bestween SNP and trait.

Pint1df

  corresponding list of P-values of signifcance of the interactions between SNPs, for the allelic model

P2df

  corresponding list of P-values of genotypic test for association bestween SNP and trait For `link{scan.haplo}` and `link{scan.haplo.2D}` this is equal to P1df and has nothing to do with the actual degrees fo freedom of the test

Pint1df

  corresponding list of P-values of signifcance of the interactions between SNPs for the genotypic test

medChi1df

  Median Chi-square for allelic test

medChi2df

  Median Chi-square on genotypic test

map

  list of map positions of the SNPs

chromosome

  list of chromosomes the SNPs belong to

formula

  which formula/function call was used to comput P-values

family

  family of the link function / nature if the test

idnames

  list of people used in analysis

### Methods

plot

  `signature(object = "scan.gwaa.2D")`: Plots summary of 2D scan, using lsit element P1df

### Author(s)

Yurii Aulchenko

### See Also

`scan.gwaa.2D-class`, `scan.glm.2D`, `scan.haplo.2D`, `plot.scan.gwaa.2D`

### Examples

    require(GenABEL.data)
    data(srdta)
    sc <- scan.glm.2D("qt3~CRSNP",data=srdta,snps=c(1:10))
    class(sc)
    sc$P1df
    sc$P2df
    sc
    plot(sc)

[Package GenABEL version 1.8-0 Index]