Description Usage Arguments Value Author(s) References See Also Examples
Generates a SAM plot for a specified value of Delta.
1 2 3 |
object |
an object of class SAM. |
delta |
a numeric value specifying the value of Delta for which the SAM plot should be generated. |
pos.stats |
an integer between 0 and 2. If |
sig.col |
a specification of the color of the significant genes. If |
xlim |
a numeric vector of length 2 specifying the x limits (minimum and maximum) of the plot. |
ylim |
a numeric vector of length 2 specifying the y limits of the plot. |
main |
a character string naming the main title of the plot. |
xlab |
a character string naming the label of the x axis. |
ylab |
a character string naming the label of the y axis. |
pty |
a character specifying the type of plot region to be used. |
lab |
a numeric vector of length 3 specifying the approximate number of tickmarks on the x axis and on the y axis and the label size. |
pch |
either an integer specifying a symbol or a single character to be used as the
default in plotting points. For a description of how |
sig.cex |
a numerical value giving the amount by which the symbols of the significant genes should be scaled relative to the default. |
... |
further graphical parameters. See |
A SAM plot.
Holger Schwender, holger.schw@gmx.de
Tusher, V.G., Tibshirani, R., and Chu, G. (2001). Significance analysis of microarrays applied to the ionizing radiation response. PNAS, 98, 5116-5121.
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 | ## Not run:
# Load the package multtest and the data of Golub et al. (1999)
# contained in multtest.
library(multtest)
data(golub)
# Perform a SAM analysis for the two class unpaired case assuming
# unequal variances.
sam.out <- sam(golub, golub.cl, B=100, rand=123)
# Generate a SAM plot for Delta = 2
sam.plot2(sam.out, 2)
# Alternatively way of generating the same SAM plot
plot(sam.out, 2)
# As an alternative, the MD plot can be generated.
md.plot(sam.out, 2)
## End(Not run)
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