Isofudge {IsoGene}R Documentation

Calculation of the fudge factor for the five SAM test statistics in the SAM procedure

Description

The function calculates the fudge factor for SAM test statistics for the five test statistics (the global likelihood test, Williams, Marcus, M, and the modified M).

Usage

  Isofudge(x, y)

Arguments

x indicates the dose levels
y gene expression for all genes

Value

A vector of five fudge factor values for the five SAM test statistics.

Note

This function calculates the fudge factor for SAM test statistics for the five test statistics.

Author(s)

Lin et al.

See Also

isoreg, Isoallfdr, IsoGenemSAM, Isoqqstat, Isoqval,IsoTestSAM,IsoSAMPlot

Examples

  set.seed(1234)
  x <- c(rep(1,3), rep(2,3), rep(3,3))
  y1 <- matrix(rnorm(9000, 1,1), 1000, 9)   # 1000 genes with no trends
  y2 <- matrix(c(rnorm(3000, 1,1), rnorm(3000,2,1), rnorm(3000,3,1)),
               1000, 9)  # 1000 genes with increasing trends
  y <- data.frame(rbind(y1, y2))  # y needs to be a data frame
  fudge.factor <- Isofudge(x,y)

[Package IsoGene version 1.0-14 Index]