List of the significant genes

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Description

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

Usage

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

Arguments

object

either a SAM- or an EBAM-object.

delta

a numeric value specifying the threshold Delta in the SAM or EBAM analysis. Note that the meaning of Delta differs between SAM and EBAM: In SAM, it is a strictly positive value, whereas in EBAM it is a probability.

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 or ebam, respectively.

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, the header specifies the type of analysis and the used value of Delta. To avoid a header, set text = "".

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, ebam

Examples

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## 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)

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