maigesRelNetB-class: maigesRelNetB class, store results of relevance network...

In maigesPack: Functions to handle cDNA microarray data, including several methods of data analysis

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).

type:

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 <[e-mail]>

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.

maigesPack documentation built on Nov. 8, 2020, 6:23 p.m.