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 1.4-2
Index]