Class "scan.gwaa"

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
[
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

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

[Package GenABEL version 1.6-7 Index]