scan.gwaa-class: Class "scan.gwaa"
In GenABEL: genome-wide SNP association analysis

Description Names Methods Author(s) See Also Examples

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.

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

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

Yurii Aulchenko

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

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

Loading required package: MASS
Loading required package: GenABEL.data
Warning messages:
1: In qtscore(qt3, data = srdta, snps = c(1:10)) :
  11 observations deleted due to missingness
2: In qtscore(qt3, data = srdta, snps = c(1:10)) :
  Number of observations < 100, Lambda estimate is unreliable
3: In qtscore(qt3, data = srdta, snps = c(1:10)) :
  Lambda estimated < 1, set to 1
[1] "scan.gwaa"
attr(,"package")
[1] "GenABEL"
 [1] 0.6206631 0.9213793 0.4251905 0.4294288 0.1198121 0.5191618 0.8107706
 [8] 0.6362554 0.9243949 0.9661461
 [1] 0.1439832 0.9410801 0.0917089 0.5468608 0.2434075 0.5306268 0.4335132
 [8] 0.6085958 0.9949356 0.9683563
***** 'scan.gwaa' object *****
*** Produced with:
qtscore(formula = qt3, data = srdta, snpsubset = c(1:10))
*** Test used: gaussian 
*** no. IDs used: 2489 ( p1 p2 p3 , ... )
*** Lambda: 1 
*** Results table contains 10 rows and 9 columns
      Chromosome Position Strand A1 A2    N         effB    se_effB    chi2.1df
rs10           1     2500      +  T  G 2374  0.023464694 0.04741197 0.244936670
rs18           1     3500      +  G  A 2374 -0.003500682 0.03546917 0.009740993
rs29           1     5750      -  G  T 2364  0.037311507 0.04678860 0.635924486
rs65           1    13500      +  A  T 2368  0.028309255 0.03582681 0.624367794
rs73           1    14250      +  A  G 2375 -0.188851610 0.12140406 2.419774871
rs114          1    24500      +  A  T 2382  0.031861867 0.04942598 0.415558204
rs128          1    27000      -  G  T 2380 -0.023143838 0.09666144 0.057327665
rs130          1    27250      +  A  G 2369 -0.016360101 0.03459228 0.223673034
rs143          1    31000      +  T  G 2366 -0.003024973 0.03187565 0.009005852
rs150          1    33250      +  C  A 2358  0.001452399 0.03422051 0.001801354
           P1df        effAB        effBB   chi2.2df      P2df     Pc1df
rs10  0.6206631  0.071615177 -0.240840767 3.87611759 0.1439832 0.6206631
rs18  0.9213793  0.006817110 -0.023716040 0.12145406 0.9410801 0.9213793
rs29  0.4251905  0.089232254 -0.219461167 4.77827171 0.0917089 0.4251905
rs65  0.4294288 -0.034094995  0.017970471 1.20712189 0.5468608 0.4294288
rs73  0.1198121 -0.262479535 -0.217934080 2.82603627 0.2434075 0.1198121
rs114 0.5191618  0.055535069 -0.088809396 1.26739272 0.5306268 0.5191618
rs128 0.8107706  0.050057879 -0.446498776 1.67166603 0.4335132 0.8107706
rs130 0.6362554  0.048341579  0.003532344 0.99320185 0.6085958 0.6362554
rs143 0.9243949 -0.001558796 -0.006191393 0.01015456 0.9949356 0.9243949
rs150 0.9661461  0.018349298  0.011252223 0.06431026 0.9683563 0.9661461
___ Use 'results(object)' to get complete results table ___