discrete.BH {DiscreteFDR} | R Documentation |
Apply the [HSU], [HSD], [AHSU] and [AHSD] procedures, with or without computing the critical constants, to a set of p-values and their discrete support.
discrete.BH(raw.pvalues, pCDFlist, alpha = 0.05, direction = "su", adaptive = FALSE, ret.crit.consts = FALSE) DBH(raw.pvalues, pCDFlist, alpha = 0.05, direction = "su", ret.crit.consts = FALSE) ADBH(raw.pvalues, pCDFlist, alpha = 0.05, direction = "su", ret.crit.consts = FALSE)
raw.pvalues |
vector of the raw observed p-values, as provided by the end user and before matching with their nearest neighbour in the CDFs supports. |
pCDFlist |
a list of the supports of the CDFs of the p-values. Each support is represented by a vector that must be in increasing order. |
alpha |
the target FDR level, a number strictly between 0 and 1. For |
direction |
a character string specifying whether to conduct a step-up ( |
adaptive |
a boolean specifying whether to conduct an adaptive procedure or not. |
ret.crit.consts |
a boolean. If |
DBH
and ADBH
are wrapper functions for discrete.BH
.
DBH
simply passes all its parameters to discrete.BH
with adaptive = FALSE
.
ADBH
does the same with adaptive = TRUE
.
This version: 2019-06-18.
A DiscreteFDR
S3 class object whose elements are:
Rejected |
Rejected raw p-values |
Indices |
Indices of rejected hypotheses |
Num.rejected |
Number of rejections |
Adjusted |
Adjusted p-values (only for step-down direction). |
Critical.constants |
Critical constants (if requested) |
Method |
Character string describing the used algorithm, e.g. 'Discrete Benjamini-Hochberg procedure (step-up)' |
Signif.level |
Significance level |
Data$raw.pvalues |
The values of |
Data$pCDFlist |
The values of |
Data$data.name |
The respective variable names of |
X1 <- c(4, 2, 2, 14, 6, 9, 4, 0, 1) X2 <- c(0, 0, 1, 3, 2, 1, 2, 2, 2) N1 <- rep(148, 9) N2 <- rep(132, 9) Y1 <- N1 - X1 Y2 <- N2 - X2 df <- data.frame(X1, Y1, X2, Y2) df #Construction of the p-values and their support df.formatted <- fisher.pvalues.support(counts = df, input = "noassoc") raw.pvalues <- df.formatted$raw pCDFlist <- df.formatted$support DBH.su.fast <- DBH(raw.pvalues, pCDFlist) summary(DBH.su.fast) DBH.sd.fast <- DBH(raw.pvalues, pCDFlist, direction = "sd") DBH.sd.fast$Adjusted summary(DBH.sd.fast) DBH.su.crit <- DBH(raw.pvalues, pCDFlist, ret.crit.consts = TRUE) summary(DBH.su.crit) DBH.sd.crit <- DBH(raw.pvalues, pCDFlist, direction = "sd", ret.crit.consts = TRUE) DBH.sd.crit$Adjusted summary(DBH.su.crit) ADBH.su.fast <- ADBH(raw.pvalues, pCDFlist) summary(ADBH.su.fast) ADBH.sd.fast <- ADBH(raw.pvalues, pCDFlist, direction = "sd") ADBH.sd.fast$Adjusted summary(ADBH.sd.fast) ADBH.su.crit <- ADBH(raw.pvalues, pCDFlist, ret.crit.consts = TRUE) summary(ADBH.su.crit) ADBH.sd.crit <- ADBH(raw.pvalues, pCDFlist, direction = "sd", ret.crit.consts = TRUE) ADBH.sd.crit$Adjusted summary(ADBH.sd.crit)