list.siggenes {siggenes} | R Documentation

## List of the significant genes

### Description

Lists the genes called differentially expressed by the SAM or the EBAM 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` | 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

    ## 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 1.58.0 Index]