Isoqval {IsoGene}R Documentation

Obtaining the list of significant genes using the SAM procedure

Description

The function obtains the list of significant genes using the SAM procedure for the five test statistics (the global likelihood test, Williams, Marcus, M, and the modified M).

Usage

Isoqval(delta, allfdr, qqstat, stat)

Arguments

delta the delta value as cut-off to find the number of significant genes
allfdr the delta table obtained from function Isoallfdr
qqstat output from function Isoqqstat containing the test statistics of permutations
stat choose one of the five test statistics to use

Value

A list of components

res returns the list genes with descending q-values of the SAM procedure in three columns: the first column is the row number of the genes, the second column is the observed test statistic values, and the last column is the q-values
sign.list returns the list of significant genes found by the defined delta value with descending p-values in three columns: the first column is the row number of the genes, the second column is the observed test statistic values, and the last column is the q-values

Note

This function obtains the list of significant genes using the SAM procedure for the five test statistics. To use the SAM procedure, the number of genes in the dataset is preferably larger than 500.

Author(s)

Lin et al.

See Also

isoreg, Isoqqstat, Isoallfdr, IsoTestSAM, IsoSAMPlot

Examples

  set.seed(1234)
  x <- c(rep(1,3),rep(2,3),rep(3,3))
  y1 <- matrix(rnorm(4500, 1,1),500,9) ## 500 genes with no trends
  y2 <- matrix(c(rnorm(1500, 1,1),rnorm(1500,2,1),rnorm(1500,3,1)),500,9) ## 500 genes with increasing trends
  y <- data.frame(rbind(y1, y2)) ##y needs to be a data frame
  qqstat <- Isoqqstat(x, y, fudge="pooled", niter=100)
  allfdr <- Isoallfdr(qqstat, ,stat="E2")
  qval <- Isoqval(delta=0.2, allfdr, qqstat, stat="E2")

[Package IsoGene version 1.0-15 Index]