R: 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

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

[Package GenABEL version 1.8-0 Index]