identify {siggenes}R Documentation

SAM specific identify method


Obtaining gene-specific information on a gene by clicking on the corresponding point in the SAM plot


identify(x, showText = TRUE, getInfo = TRUE, pos = 4, cex = 0.8, add.xy = numeric(2), 
	n.digits = 3, ask = FALSE, ll = FALSE, browse = FALSE, chip= "", ...)


x a SAM object
showText logical indicating if the gene name should be plotted near the identified point
pos numerical value specifying the place where the gene name is plotted. Default is 4 (to the right of the point). For details and other specifications see ?text
cex numerical value specifying the relative size of the plotted text. For details see ?par
add,xy a numerical vector of length 2. The text is plotted add.xy[1] units in x-direction and add.xy[2] units in the y-direction from the position where it is plotted by default
n.digits integer specifying the number of decimal places in the output
ask logical indicating if the user should be asked before the next point can be identified
ll logical indicating if both the locus links and the symbols of the genes should be added to the output
browse logical indicating if the NCBI webpage corresponding to the locus link of the identified point is opened. Ignored if ll=FALSE
chip character string specifying the chip type used in this analysis. Ignored if ll=FALSE, If the argument data in sam(data,cl,...) has been specified by an ExpressionSet object chip need not to be specified
>code>... further options such as col for the plotted text. See ?text


SAM was deveoped by Tusher et al. (2001).

!!! There is a patent pending for the SAM technology at Stanford University. !!!


Holger Schwender,


Tusher, V.G., Tibshirani, R., and Chu, G. (2001). Significance analysis of microarrays applied to the ionizing radiation response. PNAS, 98, 5116-5121.

See Also

sam, SAM-class, summary