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

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 1.6-7 Index]