scan.gwaa-class {GenABEL} | R Documentation |
Class "scan.gwaa"
Description
This class contains results of GWA analysis. This is
an list object, generated by scan.glm
, scan.haplo
, ccfast
,
qtscore
, emp.ccfast
, or emp.qtscore
.
Names
- snpnames
- list of names of SNPs tested
- P1df
- corresponding list of P-values of 1-d.f. (additive or allelic)
test for association bestween SNP and trait
- P2df
- corresponding list of P-values of 2-d.f. (genotypic) test for
association bestween SNP and trait
- Pc1df
- P-values from the 1-d.f. test for association bestween SNP
and trait; the statistics is corrected for possible
inflation
- effB
- Effect of the B allele in allelic test (OR for
ccfast
, difference from the mean for qtscore
and beta from the scan.glm
)
- effAB
- Effect of the AB genotype in genotypic test
- effBB
- Effect of the BB genotype in genotypic test
- map
- list of map positions of the SNPs
- chromosome
- list of chromosomes the SNPs belong to
- idnames
- list of people used in analysis
- lambda
- list with elements "estimate" (inflation factor estimate, as
computed using lower 90 percents of the distribution) and
"se" (standard error of the estimate)
- formula
- which formula/function call was used to comput P-values
- family
- family of the link function / nature of the test
Methods
- plot
signature(object = "scan.gwaa")
:
Plots summary of GWAA
Author(s)
Yurii Aulchenko
See Also
ccfast
,
qtscore
,
scan.glm
,
scan.haplo
,
emp.ccfast
,
emp.qtscore
,
estlambda
,
plot.scan.gwaa
Examples
data(srdta)
sc <- scan.glm("qt3~CRSNP",data=srdta,snps=c(1:10))
class(sc)
sc$P1df
sc$P2df
sc
plot(sc)
[Package
GenABEL version 1.4-2
Index]