scan.gwaa.2D-class: Class "scan.gwaa.2D"

In GenABEL: genome-wide SNP association analysis

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)

GenABEL documentation built on May 30, 2017, 3:36 a.m.