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

[

signature(object = "scan.gwaa", i = "ANY", j = "ANY", drop = "ANY"): subsetting operation

annotation

signature(object = "scan.gwaa"): extracts annotation

idnames

signature(object = "scan.gwaa"): extracts id names

snpnames

signature(object = "scan.gwaa"): extracts snp names

nids

signature(object = "scan.gwaa"): extracts number of ids

nsnps

signature(object = "scan.gwaa"): extracts number of snps

map

signature(object = "scan.gwaa"): extracts map

chromosome

signature(object = "scan.gwaa"): extracts chromosome

strand

signature(object = "scan.gwaa"): extracts strand

coding

signature(object = "scan.gwaa"): extracts coding

refallele

signature(object = "scan.gwaa"): extracts reference allele

effallele

signature(object = "scan.gwaa"): extracts effective allele

male

signature(object = "scan.gwaa"): extracts male indicator

Author(s)

Yurii Aulchenko

See Also

ccfast, qtscore, scan.glm, scan.haplo, emp.ccfast, emp.qtscore, estlambda, plot.scan.gwaa

Examples

require(GenABEL.data)
data(srdta)
sc <- qtscore(qt3,data=srdta,snps=c(1:10))
class(sc)
sc[,"P1df"]
sc[,"P2df"]
sc
plot(sc)