rppa2boxplot: Draws boxplots of groups of an RPPA data set including wilcox...

In RPPanalyzer: Reads, Annotates, and Normalizes Reverse Phase Protein Array Data

Draws boxplots of groups of an RPPA data set including wilcox or kruskal test.

Description

Draws boxplots of groups of an RPPA data set and compares the expression values to a reference group (control) if provided (wilcox.test). Otherwise a test on general differences is performed (kruskal.test). Additionally a grouping order for plotting can be provided here.

Usage

rppa2boxplot(x, param, control=NULL, orderGrp=NULL, file = "boxplot_groups.pdf")

Arguments

x	List with RPPA data with aggregated replicate spots
param	Character value of one of the columns of the sampledescription matrix, i.e. x[[4]], describing the phenodata that should be analyzed
control	Character value of one of the columns of the sampledescription matrix, i.e. x[[4]], describing the sample group of param that serves as reference in the wilcoxon test. In case of NULL (default) the general kruskal.test is performed instead.
orderGrp	defines the ordering of the subgroups in param, i.e. vector of specifically ordered values of param
file	Title of the file that will be exported.

Value

Generates a PDF file

Author(s)

Silvia von der Heyde, Heiko Mannsperger

Examples

## Not run: 
library(RPPanalyzer)
	
data(dataIII)
dataIII_median <- sample.median(dataIII)
rppa2boxplot(x=dataIII_median, param="rank", control="vx",
	orderGrp=c("vx","zx","yzr","rxi"), file="wilcoxonBoxplot.pdf")
rppa2boxplot(x=dataIII_median, param="rank", control=NULL,
	orderGrp=c("vx","zx","yzr","rxi"), file="kruskalBoxplot.pdf")

## End(Not run)

RPPanalyzer documentation built on Aug. 28, 2023, 5:07 p.m.