Description Usage Arguments Value Note Author(s) References See Also Examples
Expected LFDR (ELFDR) of HBE with empirical estimation of the null hypothesis distribution (HBEE) from function lfdr.empiricalNull
.
1 2 |
stat |
Input numeric vector of statistics. At least one of the inputs (pvalue or stat) must be non null. |
pvalue |
Optional input numeric vector of p-values. At least one of the inputs (pvalue or stat) must be non null. If the non empty input is a vector of p-values, the function qnorm is applied to it (see manual of package |
nulltype |
Parameter for selection of the type of null hypothesis distribution in Efrons method. The value nulltype = 1 is the default in |
bre |
Number of breaks in the discretization of the z-score axis in Efrons method (see package |
df |
Degrees of freedom for fitting the estimated density f(z) in Efrons method (see package |
plot |
Optional. If |
... |
Further arguments to pass to function |
A list with:
LFDR.hat |
Vector of estimates of the HBE. |
p0.hat |
Estimated proportion of unaffected features p0 (null hypothesis). |
stat |
Input vector of statistics. |
info |
Method name and information about computation failure. |
If computation fails for all features, p0.hat
is set to NA and LFDR.hat
is set to a vector of NA with lengh equal to the number of features. If it fails for a given feature, only the resulting LFDR
for that feature is set to NA. Error messages are not suppressed.
Code: David R. Bickel and Marta Padilla (modifications),
Documentation: Alaa Ali, Kyle Leckett, Marta Padilla.
Padilla, M., & Bickel, D. R. (2012). Estimators of the local false discovery rate designed for small numbers of tests. Statistical Applications in Genetics and Molecular Biology, 11(5), art. 4.
Function lfdr.empiricalNull
.
1 2 3 4 5 6 7 | # a statistic vector with missing elements
ss <- runif(55,-1,5) ;ss[c(13,2,5)]<-NA
# a p-values vector with missing elements
pp <- runif(55) ;pp[c(13,2,5)]<-NA
z1 <- lfdr.elfdr(stat = ss, df = 3)
z2 <- lfdr.elfdr(pvalue = pp, df = 3)
|
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