| scan.gwaa.2D-class {GenABEL} | R Documentation |
This class contains results of 2D analysis. This is
an list object, generated by scan.glm.2D or scan.haplo.2D.
list of names of SNPs tested
corresponding list of P-values of allelic test for association bestween SNP and trait.
corresponding list of P-values of signifcance of the interactions between SNPs, for the allelic model
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
corresponding list of P-values of signifcance of the interactions between SNPs for the genotypic test
Median Chi-square for allelic test
Median Chi-square on genotypic test
list of map positions of the SNPs
list of chromosomes the SNPs belong to
which formula/function call was used to comput P-values
family of the link function / nature if the test
list of people used in analysis
signature(object = "scan.gwaa.2D"):
Plots summary of 2D scan, using lsit element P1df
Yurii Aulchenko
scan.gwaa.2D-class,
scan.glm.2D,
scan.haplo.2D,
plot.scan.gwaa.2D
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)