Makesense {geneplotter}R Documentation

Produce Smoothed Sense/Anti-sense For All Chromosomes

Description

'Makesense' takes either an exprSet object or a matrix of gene expressions and will produce a smoothed positive and negative strands for all chromosomes.

Usage

Makesense(expr, lib, f)

Arguments

expr Either an exprSet object or a matrix of gene expressions with genes as rows and columns as samples.
lib The name of the Bioconductor annotation data package that will be used to provide mappings from probes to chromosomal locations, such as hgu95av2 or hgu133a. If expr is an exprSet, the argument defaults to the annotation slot of the exprSet.
f the smoother span to be passed to 'lowess'. Its value should be in the interval of (0,1). This gives the proportion of points in the plot which influence the smooth at each value. Larger values give more smoothness. The default value for this argument is 1/10.

Details

The expr argument can either be of class exprSet or matrix, where the latter represents the matrix of gene expressions.

If the expr argument is an exprSet, the lib argument will use the annotation slot. Users can override this behaviour and supply their own lib argument if they wish. If the exprSet has no value associated with the annotation slot (which should not happen, but is possible) then the user must supply the lib argument manually or the function will throw an error.

Value

A list of 2 components:

ans2 a list, whose components correspond to samples in the same order as appearing in the columns of 'expr'. Each component is also a list, named by chromosomes "1"-"22", "X" and "Y". Each named component is again a list with two elements named "posS" and "negS", corresponding to the positive and negative strands of a chromosome, each of which isan object returned by 'lowess'.
lib as passed in.

Author(s)

Robert Gentleman and Xiaochun Li

See Also

plotChr

Examples

require("hgu133a") ||
stop("\nThis example requires the hgu133a package which is not installed.",
     "\nPlease install the package (perhaps using: ",
     "install.packages2(\"hgu133a\")) and try again")

data(eset133a)

esetobj <- Makesense(exprs(eset133a), "hgu133a")

esetobj2 <- Makesense(eset133a, "hgu133a")

[Package geneplotter version 1.8.0 Index]