boxplot-methods: Method boxplot for objects defined in this package

In maigesPack: Functions to handle cDNA microarray data, including several methods of data analysis

Description

Generic function boxplot to display boxplots of the data.

Usage

## S3 method for class 'maigesRaw'
boxplot(x, ...)

## S3 method for class 'maiges'
boxplot(x, name=NULL, gLabelID=NULL, sLabelID=NULL, gSamples=NULL, ...)

## S3 method for class 'maigesANOVA'
boxplot(x, name=NULL, gLabelID=NULL, sLabelID=NULL, gSamples=NULL, ...)

## S3 method for class 'maigesDEcluster'
boxplot(x, name=NULL, gLabelID=NULL, sLabelID=NULL, gSamples=NULL, ...)

Arguments

x	an object of any class defined in this package
name	character string specifying a gene to do boxplot of their expression values along the types specified by sLabelID.
gLabelID	character value giving the name of gene label to be used to search for parameter name.
sLabelID	idem to gLabelID, specifying the name of sample label to be used to separate the gene observations.
gSamples	a named list containing character vectors defining groups of samples from sLabelID.
...	additional parameters to boxplot method defined in graphics package or to maBoxplot method defined in marray package (for maigesRaw, maiges or maigesANOVA classes), in this case the additional parameters must not be named, because these names conflict with the boxplot generic function definition.

Details

This method uses the function maBoxplot from marray package to show boxplots of the W values along all the slides of a dataset or along specific accessor methods to stratify the data in objects of class maigesRaw. For objects of classes maiges or maigesANOVA this is also done if the argument name is NULL, else the method shows boxplots for the expression values of the gene specified by name stratified by sample types from sLabelID. For objects of class maigesDEcluster only boxplots of genes are produced and the argument name may not be NULL.

If you especify the y parameter (but not named), defined for the method maBoxplot in package marray, it will be displayed the M values instead of W.

Author(s)

Gustavo H. Esteves <[e-mail]>

See Also

maBoxplot in the marray package and boxplot in the graphics package.

Examples

## Loading the dataset
data(gastro)

## To see the boxplots for W values in all chips
boxplot(gastro.raw)  ## maigesRaw class
boxplot(gastro.norm) ## maigesNorm class
boxplot(gastro.summ) ## summarized data (also maigesNorm class)

## To see the boxplots for W values in individual chips
## separating into print tips.
boxplot(gastro.raw[,1])  ## maigesRaw class, first chip
boxplot(gastro.norm[,8]) ## maigesNorm class, 8th chip
boxplot(gastro.summ[,19]) ## summarized data (also maigesNorm class), 19th chip


## Boxplot for individual genes into ANOVA model fitting
gastro.ANOVA = designANOVA(gastro.summ, factors="Tissue")
gastro.ANOVAfit = deGenesANOVA(gastro.ANOVA, retF=TRUE)

boxplot(gastro.ANOVAfit, name="KLK13", gLabelID="GeneName", 
sLabelID="Tissue")

maigesPack documentation built on Nov. 8, 2020, 6:23 p.m.