TopK.test: TopK exact test (main function)

In ziqiangc/TopK: TopK Exact Test

Description

This function perform TopK exact test on a two group data set (Case-Control study). The univariate p-values were calculated based on mulitiple choices of test.

Usage

TopK.test(x, g, Kvals = c(1, 2, 3, 4, 5, 10, 25), method = c("WRS",
  "t.test"), B = 0, alternative = c("two.sided", "less", "greater"),
  ties.method = c("random", "min", "max", "average"), pval = FALSE,
  ReturnType = "TopK", vrb = T)

Arguments

x	a data matrix containing features as rows and samples as columns.
g	a vector or factor object giving the group for the corresponding samples of x.
Kvals	a numeric vector indicating how many "K" we choose.
method	a character string specifying which method used in TopK test, must be one of "WRS" (default) and "t.test". See detail.
B	the number of inner permutation, default is "0" for exact test.
alternative	a character string specifying the alternative hypothesis, must be one of "two.sided" (default), "greater" or "less". You can specify just the initial letter.
ties.method	a character string specifying how ties are treated, see <e2><80><98>Details<e2><80><99>; can be abbreviated.
pval	Only option for permutation test method. If TRUE, the permutation matrix will be populated by p-values from t-test. If FALSE, the permutation matrix will be directly populated by t statistics (negative absolute value).
ReturnType	character(1) specify how to return the results. Could be "list", "vector" or rich format "TopK". See detail.
vrb	a logical vector indicating TRUE when show some words while running, FALSE otherwise.

Examples

TopK.test(x,g,method="WRS")

ziqiangc/TopK documentation built on May 4, 2019, 11:23 p.m.