maigesRelNetB-class:
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.
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.
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).
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)