R/other.oneside.pvalues.R

In metaSeq: Meta-analysis of RNA-Seq count data in multiple studies

other.oneside.pvalues <-
function (Upper, Lower, weight = NULL) 
{
    if ((min(!is.na(Upper)) < 0) || (max(!is.na(Upper)) > 1)) {
        stop("Is this dataset (upper) pvalues? Some elements exceed 0 - 1 range. Please confirm first.\n")
    }
    if ((min(!is.na(Lower)) < 0) || (max(!is.na(Lower)) > 1)) {
        stop("Is this dataset (lower) pvalues? Some elements exceed 0 - 1 range. Please confirm first.\n")
    }
    if (nrow(Upper) != nrow(Lower)) {
        stop("Number of rows in upper p-values and lower p-values are different!\n")
    }
    if (ncol(Upper) != ncol(Lower)) {
        stop("Number of columns in upper p-values and lower p-values are different!\n")
    }
    if ((!is.null(weight)) && (ncol(Upper) != length(weight))) {
        A <- ncol(Upper)
        B <- length(weight)
        Call <- paste0("Number of column in p-value matrix is ", 
            A, " but length of weight vector is ", B, ". Please confirm first.\n")
        stop(Call)
    }
    l <- ncol(Upper)
    out <- sapply(1:l, function(x) {
        output <- list()
        length(output) <- 3
        names(output) <- c("upper", "lower", "weight")
        U <- Upper[, x]
        L <- Lower[, x]
        names(U) <- rownames(Upper)
        names(L) <- rownames(Lower)
        output$upper <- U
        output$lower <- L
        output$weight <- weight[x]
        return(output)
    })
    colnames(out) <- paste("Exp", 1:l)
    return(out)
}