maigesRelNetB-class {maigesPack} | R Documentation

## maigesRelNetB class, store results of relevance network analysis (Butte's method)

### Description

This class defines a structure to store the results of relevance network analysis, using a method that was proposed by Butte et al. (2000), see the reference below. Objects of this type are generated calling the function `relNetworkB`.

### Details

Objects of this class are produced by calling the function `relNetworkB` over an object of class `maiges` to search for pairs of genes with significant correlation values in a specific sample type, according to the method proposed by Butte et al. (2000).

### Slots

`W`:
  numeric matrix giving the W values of the genes tested. This information is useful for doing plots representing the correlation coefficient values.
`Corr`:
  numerical square matrix that store the correlation coefficient values between all pair of genes tested.
`Pval`:
  numerical square matrix that store the p-value for each correlation value between the pairs of genes.
`maxB`:
  numerical square matrix that store the maximum (in absolute value) of the correlation values calculated by permutation values, as described by Butte et al. (2000).
`types`:
  character vector giving the name of sample type tested.
`Slabel`:
  string with the sample label used to define the sample types tested.
`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 = 'maigesRelNetB')`: image method for `maigesRelNetB` class. Display colour representation of the correlation matrix.
plot
  `signature(x = 'maigesRelNetB')`: plot method for `maigesRelNetB` class. Display a circular graph representing the relevance network.
print
  `signature(x = 'maigesRelNetB')`: print method for `maigesRelNetB` class.
show
  `signature(x = 'maigesRelNetB')`: show method for `maigesRelNetB` class.
summary
  `signature(x = 'maigesRelNetB')`: summary method for `maigesRelNetB` class.

### Author(s)

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

### References

Butte, A.J.; Tamayo, P.; Slonim, D.; Golub, T.R. and Kohane, I.S. Discovering functional relationships between RNA expression and chemotherapeutic susceptibility using relevance networks. PNAS, 97, 12182-12186, 2000. (http://www.pnas.org/cgi/content/full/97/22/12182)

### See Also

`relNetworkB`.

[Package maigesPack version 1.2.1 Index]