Description Usage Arguments Value Author(s) See Also Examples
Lists the genes called differentially expressed by the SAM or the EBAM analysis for a specified value of the threshold Delta.
1 2 |
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 |
gene.names |
a character vector containing the names of the genes. Needs
only to be specified, if the gene names were not specified in |
order |
if |
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 |
append |
If |
A list of significant genes either shown in the console or stored in a file.
Holger Schwender, holger.schw@gmx.de
1 2 3 4 5 6 7 8 9 10 11 12 13 | ## 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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