R: SAM specific identify method

identify {siggenes}

R Documentation

SAM specific identify method

Description

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

Usage

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= "", ...)

Arguments

`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`

Note

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

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

Author(s)

Holger Schwender, [email protected]

References

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