setGpar {plgem} | R Documentation

## Set graphical parameters for PLGEM fitting evaluation plots

### Description

Function to set graphical parameters for PLGEM fitting evaluation plots produced by function `plgem.fit`.

### Usage

      setGpar(minLnM=NULL, maxLnM=NULL, minLnSD=NULL, maxLnSD=NULL,
        minRes=NULL, maxRes=NULL)

### Arguments

`minLnM` | minimum 'ln(mean)' value in upper left plot.
`maxLnM` | maximum 'ln(mean)' value in upper left plot.
`minLnSD` | minimum 'ln(sd)' value in upper left plot.
`maxLnSD` | maximum 'ln(sd)' value in upper left plot.
`minRes` | minimum 'residual' value in upper right plot.
`maxRes` | maximum 'residual' value in upper right plot.

### Details

A call to `setGpar()` is the recommended way to set graphical parameters in `plgem.fit`. If parameters are left unspecified, suitable defaults will be found by `plgem.fit`.

### Value

A `list` of six elements:

`minLnM` | minimum 'ln(mean)' value in upper left plot.
`maxLnM` | maximum 'ln(mean)' value in upper left plot.
`minLnSD` | minimum 'ln(sd)' value in upper left plot.
`maxLnSD` | maximum 'ln(sd)' value in upper left plot.
`minRes` | minimum 'residual' value in upper right plot.
`maxRes` | maximum 'residual' value in upper right plot.

### Author(s)

Norman Pavelka normanpavelka@gmail.com

### References

Pavelka N, Pelizzola M, Vizzardelli C, Capozzoli M, Splendiani A, Granucci F, Ricciardi-Castagnoli P. A power law global error model for the identification of differentially expressed genes in microarray data. BMC Bioinformatics. 2004 Dec 17; 5:203; http://www.biomedcentral.com/1471-2105/5/203.

Pavelka N, Fournier ML, Swanson SK, Pelizzola M, Ricciardi-Castagnoli P, Florens L, Washburn MP. Statistical similarities between transcriptomics and quantitative shotgun proteomics data. Mol Cell Proteomics. 2008 Apr; 7(4):631-44; http://www.mcponline.org/cgi/content/abstract/7/4/631.

### See Also

`plgem.fit`, `run.plgem`

### Examples

      setGpar(minLnM=-1, maxLnM=8)

[Package plgem version 1.60.0 Index]