| estlambda {GenABEL} | R Documentation |
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)
estlambda(data, plot = FALSE, proportion = 1,
method = "regression", filter = TRUE, df = 1, ...)
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
require(GenABEL.data) data(srdta) pex <- summary(gtdata(srdta))[,"Pexact"] estlambda(pex, plot=TRUE) estlambda(pex, method="regression", proportion = 0.95) estlambda(pex, method="median") estlambda(pex, method="KS") a <- qtscore(bt,srdta) lambda(a)