bin_true_initial: bin_true_initial

In LyonsZhang/ProgPerm: Progressive permutation for a dynamic representation of the robustness of microbiome discoveries

Usage

bin_true_initial(variable, testdata, top_pm = 50, method = "kruskal", goodtype = "goodpvname")

Arguments

variable
testdata
top_pm
method
goodtype

Examples

##---- Should be DIRECTLY executable !! ----
##-- ==>  Define data, use random,
##--	or do  help(data=index)  for the standard data sets.

## The function is currently defined as
function (variable, testdata, top_pm = 50, method = "kruskal", 
    goodtype = "goodpvname") 
{
    response <- testdata[[variable]]
    levs <- unique(response)
    if (length(levs) != 2) {
        stop("The variable does not have two levels.")
    }
    else {
        position0 <- grep(levs[1], response)
        position1 <- grep(levs[2], response)
        fliplen <- min(length(position0), length(position1))
        N <- fliplen + 1
        n1 <- length(position0)
        n2 <- length(position1)
        testlevel <- testdata
        testlevel[[variable]] <- NULL
        n <- round((N + 1)/2)
        group <- factor(response)
        if (method == "kruskal") {
            otu.test <- apply(testlevel, 2, function(x) {
                kt <- kruskal.test(x = x, g = group)
                return(data.frame(pv = kt$p.value, es = kt$statistic/sqrt(n1^2 + 
                  n2^2)))
            })
            otu.test <- do.call(rbind, otu.test)
        }
        else if (method == "wilcox") {
            otu.test <- apply(testlevel, 2, function(x) {
                options(warn = -1)
                wt <- wilcox.test(x ~ group)
                return(data.frame(pv = wt$p.value, es = wt$statistic/sqrt(n1^2 + 
                  n2^2)))
            })
            otu.test <- do.call(rbind, otu.test)
        }
        else {
            stop("Set up method either as 'kruskal' or 'wilcox'!")
        }
        select <- switch(goodtype, goodpvname = order(otu.test$pv)[1:top_pm], 
            goodesname = order(abs(otu.test$es))[1:top_pm], stop("goodtype must be one of the follows: 'goodpvname' and 'goodesname'. "))
        selname <- row.names(otu.test)[select]
    }
    return(list(select = select, selname = selname, position0 = position0, 
        position1 = position1, levs = levs, testlevel = testlevel, 
        n = n, N = N, otu.test = otu.test))
  }

LyonsZhang/ProgPerm documentation built on July 16, 2020, 12:45 a.m.