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Test and document truncated p-values #18

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Test and document truncated p-values #18

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606104e
document truncated p-val issue
ewallace Oct 4, 2019
5dc3561
Test for truncated p-values.
ewallace Oct 4, 2019
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7 changes: 6 additions & 1 deletion R/qvalue.R
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Original file line number Diff line number Diff line change
Expand Up @@ -13,7 +13,9 @@
#' will be utilized in the internal calls made in \code{\link{qvalue}}. See \url{http://genomine.org/papers/Storey_FDR_2011.pdf}
#' for a brief introduction to FDRs and q-values.
#'
#' @param p A vector of p-values (only necessary input).
#' @param p A vector of p-values (only necessary input). Note that qvalue expects that these values are uniformly distributed
#' on [0,1), and under default parameter values will throw an error. If your p-value distribution is truncated, qvalue will
#' run with the BH procedure by setting pi0 = 1.
#' @param fdr.level A level at which to control the FDR. Must be in (0,1]. Optional; if this is
#' selected, a vector of TRUE and FALSE is returned that specifies
#' whether each q-value is less than fdr.level or not.
Expand Down Expand Up @@ -94,6 +96,9 @@ qvalue <- function(p, fdr.level = NULL, pfdr = FALSE, lfdr.out = TRUE, pi0 = NUL
} else if (!is.null(fdr.level) && (fdr.level <= 0 || fdr.level > 1)) {
stop("'fdr.level' must be in (0, 1].")
}
if ( max(p) < 0.5 && is.null(pi0) ) {
stop("p-values are truncated and pi0 not set. Try running BH procedure by setting pi0 = 1")
}

# Calculate pi0 estimate
if (is.null(pi0)) {
Expand Down