splicegear (version 1.44.0)

as.data.frame.SpliceExprSet: SpliceExprSet object to data.frame converter

Description

Converts a SpliceExprSet object to a data.frame.

Usage

"as.data.frame"(x, row.names = NA, optional = NA, ...)
"as.data.frame"(x, row.names = NA, optional = NA, ...)

Arguments

x

object SpliceSites-class or SpliceExprSet-class.

row.names

NULL or a character vector giving the row names for the data frame. Missing values are not allowed.

optional

logical. If TRUE, setting row names is optional.

...

currently ignored.

Value

A data.frame. For both functions the first column names are begin, end, isintypeI, isintypeII, exprs and genenames. In the case of as.data.frame.SpliceExprSet, the next variable names will the ones in the AnnotatedDataFrame-class attribute of the ExpressionSet-class object belonging the SpliceExprSet-class. The last variable names will be the ones in the slot info of the Probes-class object.

Details

Data are traditionally stored in objects of class data.frame. This function links the object-oriented design of the package with the large amount of functions working on data.frames.

Examples

data(spliceset)

dataf <- as.data.frame(spliceset)

lm.panel <- function(x, y, ...) {
                                  points(x,y,...)
                                  p.lm <- lm(y~x); abline(p.lm)
                                }

## probe intensity values conditioned by the position of the probes on
## the mRNA
coplot(log(exprs) ~ Material | begin, data=dataf, panel=lm.panel)