PAA (version 1.7.1)

volcanoPlot: Draw a volcano plot.

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".

Value

No value is returned.

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.

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)