maigesActMod-class {maigesPack} | R Documentation

## maigesActMod class, store results of functional classification of gene groups

### Description

This class defines a structure to store the results of functional classification of gene groups (or modules) that was proposed by Segal et al. (2004), see the reference below. Objects of this type are generated by calling the function `activeMod`.

### Details

Objects of this class are produced by calling the function `activeMod` over an object of class `maiges` to search for gene groups that present numbers of genes induced or repressed greater than the expected by chance in biological sample types of interest. This is done according to the model proposed by Segal et al. (2004), described below.

### Slots

`modBySamp`:

  numerical matrix containing the fraction of genes activated (or negative fraction of genes repressed) for all chips. The rows and columns of the matrix represents the chips and the gene groups used, respectively.

`modByCond`:

  numerical matrix storing the fraction (or negative fraction) of different sample types that presents alteration in the gene groups tested. The rows and columns represents the sample types and gene groups, respectively.

`globalScore`:

  list with the same length as the number of gene groups containing matrices with the genes as rows and 2 columns. The first column gives a global score that measure the consistency of the classification of the gene and the group, the second column gives the p-value for this score, as described in Segal et al. (2004).

`tissueScore`:

  a list similar to the previous one, but having arrays of 3 dimensions that gives scores similar to that one described above, but relating only to each specific sample type. Note that this new score was implemented in this package and not in the original Segal's work.

`Date`:

  character string giving the date and time that the object was generated.

`V.info`:

  list containg three characters. The first one is a string containing the R version used when the object was created. The second is a char vector with base packages and the last one is another char vector with additional packages and version numbers.

### Methods

image

  `signature(x = 'maigesActMod')`: image method for `maigesActMod` class. Display colour representation of the fractions of gene groups induced and repressed.

plot

  `signature(x = 'maigesActMod')`: plot method for `maigesActMod` class. Do the same as image.

print

  `signature(x = 'maigesActMod')`: print method for `maigesActMod` class.

show

  `signature(x = 'maigesActMod')`: show method for `maigesActMod` class.

summary

  `signature(x = 'maigesActMod')`: summary method for `maigesActMod` class.

### Author(s)

Gustavo H. Esteves <gesteves@vision.ime.usp.br>

### References

Segal, E.; Friedman, N.; Koller, D. and Regev, A. A module map showing conditional activity of expression modules in cancer. Nature Genetics, 36, 1090-1098, 2004. (http://www.nature.com/ng/journal/v36/n10/abs/ng1434.html)

### See Also

`activeMod`.

[Package maigesPack version 1.56.0 Index]