volcanoPlot {PAA} | R Documentation

## 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"`.

### 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, michael.turewicz@rub.de

### 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)

[Package PAA version 1.16.0 Index]