Description Usage Arguments Value Author(s) See Also Examples
Estimate the inflation factor for a distribution of P-values or 1df chi-square test. The major use of this procedure is the Genomic Control, but can also be used to visualise the distribution of P-values coming from other tests. Methods implemented include 'median' (median(chi2)/0.455...), regression (of observed onto expected) and 'KS' (optimizing the chi2.1df distribution fit by use of Kolmogorov-Smirnov test)
1 2 |
data |
A vector of reals. If all are <=1, it is assumed that this is a vector of P-values, else it is treated as a vector of chi-squares |
plot |
Whether the plot should be shown or not (default). |
proportion |
The proportion of lowest P (or chi^2) values to be used when estimating the inflation factor lambda. |
method |
"regression" (default), "median", or "KS": method to be used for lambda estimation. |
filter |
if the test statistics with 0-value of chi^2 should be excluded prior to estimation of lambda. |
df |
Number of degrees of freedom. |
... |
arguments passed to the |
A list with elements
estimate |
Estimate of lambda |
se |
Standard error of the estimate |
Yurii Aulchenko
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Loading required package: MASS
Loading required package: GenABEL.data
$estimate
[1] 1.221399
$se
[1] 0.02964587
$estimate
[1] 1.221399
$se
[1] 0.02964587
$estimate
[1] 0.9069703
$se
[1] NA
$estimate
[1] 0.5000458
$se
[1] NA
Warning message:
In estlambda(pex, method = "KS") :
using method='KS' lambda too close to limits, use other method
Warning messages:
1: In test.type(y, trait.type) : binomial trait is analysed as gaussian
2: In qtscore(bt, srdta) : 11 observations deleted due to missingness
3: In qtscore(bt, srdta) : Lambda estimated < 1, set to 1
$estimate
[1] 1
$se
[1] NA
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