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
snpnameslist of names of SNPs tested
P1dfcorresponding list of P-values of 1-d.f. (additive or allelic)
test for association bestween SNP and trait
P2dfcorresponding list of P-values of 2-d.f. (genotypic) test for
association bestween SNP and trait
Pc1dfP-values from the 1-d.f. test for association bestween SNP
and trait; the statistics is corrected for possible
inflation
effBEffect of the B allele in allelic test (OR for ccfast
, difference from the mean for qtscore
and beta from the scan.glm
)
effABEffect of the AB genotype in genotypic test
effBBEffect of the BB genotype in genotypic test
maplist of map positions of the SNPs
chromosomelist of chromosomes the SNPs belong to
idnameslist of people used in analysis
lambdalist with elements "estimate" (inflation factor estimate, as
computed using lower 90 percents of the distribution) and
"se" (standard error of the estimate)
formulawhich formula/function call was used to comput P-values
familyfamily 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 1.3-9
Index]