list.siggenes {siggenes} | R Documentation |
Lists the genes called differentially expressed by the SAM or the EBAM analysis for a specified value of the threshold Delta.
list.siggenes(object, delta, file = "", gene.names = NULL, order = TRUE, text = NULL, append = FALSE)
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 |
A list of significant genes either shown in the console or stored in a file.
Holger Schwender, holger.schw@gmx.de
## 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)