RFET {PhViD} | R Documentation |
This function proposes the Fisher's Exact Test as an alternative to the PRR and ROR methods. The statistic of interest is the P-value or the mid-P-value resulting from the test (Ahmed et al., Biometrics).
RFET(DATABASE, OR0 = 1, MIN.n11 = 1, DECISION = 1, DECISION.THRES = 0.05, MID.PVAL = FALSE)
DATABASE |
Object returned by the function as.PhViD . |
OR0 |
Value of the tested odds ratio. By default, OR0=1 . |
MIN.n11 |
Minimum number of notifications for a couple to be potentially considered as a signal. By default, MIN.n11 = 1 . |
DECISION |
Decision rule for the signal generation based on
1 = FDR (Default value) 2 = Number of signals 3 = P-values or mid-P-values. See MID.PVAL |
DECISION.THRES |
Threshold for DECISION . Ex 0.05 for FDR (DECISION =1). |
MID.PVAL |
if MID.PVAL=TRUE , the statistic of interest becomes the mid-P-values instead of the P-values resulting from the Fisher's exact test. By default MID.PVAL=FALSE . |
The FDR is estimated with the LBE procedure proposed by Dalmasso et al. (2005).
ALLSIGNALS |
Data.frame summarizing the results of all couples with at least MIN.n11 notifications ordered by RANKSTAT . It contains notably the labels, the cell counts, the expected count (n1. * n.1 / N, see as.PhViD ), RANKSTAT , the observed odds ratio (ROR), the marginal counts and the estimation of FDR. |
SIGNALS |
Same Data.frame as ALLSIGNALS but restricted to the list of generated signals. |
NB.SIGNALS |
Number of generated signals. |
INPUT.PARAM |
Parameters entered in the function. |
Ismail Ahmed & Antoine Poncet
Ahmed I, Dalmasso C, Haramburu F, Thiessard F, Broet P, Tubert-Bitter P, False Discovery Rate Estimation for Frequentist Pharmacovigilance Signal Detection Methods, Biometrics, accepted.
Dalmasso C, Broet P, Moreau T (2005), A simple procedure for estimating the false discovery rate, Bioinformatics, Bioinformatics, 21: 660 - 668.
## start #data(PhViDdata.frame) #PhViDdata <- as.PhViD(PhViDdata.frame) #res <- RFET(PhViDdata) ## end