get.phat.linear: Get the pvalue for the linear statistic

In pipeGS: Permutation p-Value Estimation for Gene Set Tests

Description

Get the pvalue for the linear statistic

Usage

get.phat.linear(x, y, method = c("phat2", "saddlepoint", "phat1", "phat3",
  "nested", "mc", "exact"), N.mc = 10^3, mc.cores = 1, N.level = 1000,
  q = 0.2, B = 5 * length(x), do.sd = FALSE)

Arguments

x	binary vector of treatment assignment
y	gene expression measurement matrix
method	method to estimate pvalue for the linear statistic
N.mc	number of mc samples is method == "mc"
mc.cores	number of cores to use in mcapply
N.level	number of samples in each level if method == "nested"
q	progression quantile if method == "nested"
B	number of burn-ins to use if method == "nested"
do.sd	logical to indicate whether calculating sd or not

Value

a list containing phat from different methods

Examples

x <- c(rep(0, 4), rep(1, 4))
y <- c(rnorm(4, 0, 1), rnorm(4, 2 ,1))
get.phat.linear(x, y, method = "saddlepoint")
get.phat.linear(x, y, method = "phat1")
get.phat.linear(x, y, method = "phat2")
get.phat.linear(x, y, method = "phat3")
get.phat.linear(x, y, method = "nested")
get.phat.linear(x, y, method = "mc")
get.phat.linear(x, y, method = "exact")
get.phat.linear(x, y, method = "saddlepoint", do.sd = TRUE)
get.phat.linear(x, y, method = "phat1", do.sd = TRUE)
get.phat.linear(x, y, method = "phat2", do.sd = TRUE)
get.phat.linear(x, y, method = "phat3", do.sd = TRUE)
get.phat.linear(x, y, method = "nested", do.sd = TRUE)
get.phat.linear(x, y, method = "mc", do.sd = TRUE)
get.phat.linear(x, y, method = "exact", do.sd = TRUE)

pipeGS documentation built on May 2, 2019, 5:58 a.m.