list.siggenes {siggenes}R Documentation

List of the significant genes

Description

Lists the genes called differentially expressed by the SAM analysis for a specified value of the threshold Delta.

Usage

  list.siggenes(object, delta, file = "", gene.names = NULL, order = TRUE, 
  text = NULL, append = FALSE)

Arguments

object a object of class SAM
delta a numeric value specifying the threshold Delta in a SAM analysis
file a character string naming a file in which the output is stored. If "", the significant genes will be shown in the console
gene.names a character vector containing the names of the genes. Needs only to be specified, if the gene names were not specified in sam
order If TRUE, the gene names will be ordered by their "significance"
text a character string specifying the heading of the gene list. By default no heading is added to the gene list
append If TRUE, the output will be appended to file. If FALSE, any existing file having the name file will be destroyed

Value

A list of significant genes either shown in the console or stored in a file.

Author(s)

Holger Schwender, holger.schw@gmx.de

See Also

SAM-class,sam

Examples

## Not run: 
  # Load the package multtest and the data of Golub et al. (1999)
  # contained in \pkg{multtest}.
  library(multtest)
  data(golub)

  # Perform a SAM analysis.
  sam.out<-sam(golub,golub.cl,B=100,rand=123)
  
  # List the genes called significant by SAM using Delta = 3.1.
  list.siggenes(sam.out,3.1,gene.names=golub.gnames[,2])
## End(Not run)

[Package siggenes version 1.4.0 Index]