as.data.frame.SpliceExprSet {splicegear}R Documentation

SpliceExprSet object to data.frame converter

Description

Converts a SpliceExprSet object to a data.frame.

Usage

## S3 method for class 'SpliceSites'
as.data.frame(x, row.names = NA, optional = NA, ...)

## S3 method for class 'SpliceExprSet'
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.

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.

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.

Author(s)

Laurent Gautier

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)
[Package splicegear version 1.54.0 Index]