volcanoPlot: Draw a volcano plot.

In PAA: PAA (Protein Array Analyzer)

Description

Draws a volcano plot to visualize differential features.

Usage

volcanoPlot(elist=NULL, group1=NULL, group2=NULL, log=NULL, method="tTest",
p.thresh=NULL, fold.thresh=NULL, output.path=NULL, tag="", mMs.matrix1=NULL,
mMs.matrix2=NULL, above=1500, between=400)

Arguments

elist	EList or EListRaw object (mandatory).
group1	vector of column names for group 1 (mandatory).
group2	vector of column names for group 2 (mandatory).
log	indicates whether the data is in log scale (mandatory; note: if TRUE log2 scale is expected; mandatory).
method	method for p-value computation: "tTest" or "mMs". Default is "tTest".
p.thresh	positive float number between 0 and 1 indicating the maximum p-value for features to be considered as differential (e.g., "0.5"). This argument is optional.
fold.thresh	float number indicating the minimum fold change for features to be considered as differential (e.g., "1.5"). This argument is optional.
output.path	string indicating a path for saving the plot (optional).
tag	string that can be used for tagging the saved plot (optional).
mMs.matrix1	a precomputed M score reference matrix (see mMsMatrix()) for group 1 (mandatory when method = "mMs").
mMs.matrix2	a precomputed M score reference matrix (see mMsMatrix()) for group 2 (mandatory when method = "mMs").
above	M score above parameter (integer). Default is "1500".
between	M score between parameter (integer). Default is "400".

Details

This function takes an EList or EListRaw object and the corresponding column name vectors to draw a volcano plot. To visualize differential features, thresholds for p-values and fold changes can be defined. Furthermore, the p-value computation method ("mMs" or "tTest") can be set. When an output path is defined (via output.path) the plot will be saved as a tiff file.

Value

No value is returned.

Author(s)

Michael Turewicz, [e-mail]

Examples

cwd <- system.file(package="PAA")
load(paste(cwd, "/extdata/Alzheimer.RData", sep=""))
elist <- elist[elist$genes$Block < 10,]
c1 <- paste(rep("AD",20), 1:20, sep="")
c2 <- paste(rep("NDC",20), 1:20, sep="")
volcanoPlot(elist=elist, group1=c1, group2=c2, log=FALSE, method="tTest",
 p.thresh=0.01, fold.thresh=2)

Example output

Loading required package: Rcpp
Warning message:
system call failed: Cannot allocate memory 

PAA documentation built on Nov. 8, 2020, 8:30 p.m.