| c212.err.cntrl {c212} | R Documentation |
Implementaion of Group Bonferroni-Hochberg procedure for control of the False Discovery Rate
Description
Common interface to the error controlling methods: Unadjutsed hypothesis testing (NOADJ), Bonferroni correction (BONF), Benjamini-Hochberg procedure (BH), Group Benjamini-Hochberg (GBH), Double False Discover Rate (DFDR), subset Benjamini-Hochberg (ssBH).
Usage
c212.err.cntrl(trial.data, alpha = 0.05, method = "NOADJ",...)
Arguments
trial.data |
File or data frame containing the p-values for the hypotheses being tested. The data must contain the following columns: B: the index or name of the groupings; p: the p-values of the hypotheses. |
alpha |
The level for error control. E.g. 0.05. |
method |
The error control procedure to be applied: "NOAD" - unadjusted testing, "BONF" - Bonferroni correction "BH" - Benjamini-Hochberg procedure "GBH" - Group Benjamini-Hochberg "DFDR" - Double False Discover Rate "ssBH" - subset Benjamini-Hochberg. |
... |
Additional optional parameter for the GBH method: pi0. |
Value
The subset of hypotheses in file or trial.data deemed significant by the Group Benjamini-Hochberg process.
Author(s)
R. Carragher
Examples
trial.data <- data.frame(B = c(1, 2, 2, 2, 2, 3, 3, 3, 3, 3, 3, 3, 4, 4, 4, 4, 4),
j = c(1, 1, 2, 3, 4, 1, 2, 3, 4, 5, 6, 7, 1, 2, 3, 4, 5),
AE = c("AE1", "AE2", "AE3", "AE4", "AE5", "AE6", "AE7", "AE8", "AE9", "AE10", "AE11",
"AE12", "AE13", "AE14", "AE15", "AE16", "AE17"),
p = c(0.135005, 0.010000, 0.001000, 0.005000, 0.153501, 0.020000, 0.0013, 0.0023,
0.011, 0.023000, 0.016, 0.0109, 0.559111, 0.751986, 0.308339, 0.837154, 0.325882))
c212.err.cntrl(trial.data = trial.data, alpha = 0.05, method = "GBH")
## Not run:
B j AE p p_weighted
1 3 1 AE6 0.020000 0.0000000000
2 3 2 AE7 0.001300 0.0000000000
3 3 3 AE8 0.002300 0.0000000000
4 3 4 AE9 0.011000 0.0000000000
5 3 5 AE10 0.023000 0.0000000000
6 3 6 AE11 0.016000 0.0000000000
7 3 7 AE12 0.010900 0.0000000000
8 2 2 AE3 0.001000 0.0003333333
9 2 3 AE4 0.005000 0.0016666667
10 2 1 AE2 0.010000 0.0033333333
11 2 4 AE5 0.153501 0.0511670000
## End(Not run)