attribute_mut_inf: calculates the mutual information between each attribute of...

In pasculescu/ClusterJudge: Judging Quality of Clustering Methods using Mutual Information

Description

calculates the mutual information based on the entropy. The mutual information of the pair of attributes A,B is mi(A,b) = H(A)+H(B) -H(cbind(A,B)) where H is the entropy.

Usage

    attribute_mut_inf(entity.attribute, show.progress = FALSE, alternative.calc = FALSE)

Arguments

entity.attribute	data frame or matrix with 2 columns The assumption is that first column represent some 'entities' like gene names or gene ids. And the second column represents ‘attributes' of entities (for example Gene Ontology ID ’GO:0007260' which is 'tyrosine phosphorylation of STAT protein')
show.progress	if set to TRUE will try to show periodically the estimated percentage of completion. Note that calculation of mutual information between Gene Ontology (GO) attributes takes a long time. We already have precalculated the GO mutual information for Yeast
alternative.calc	logical that if set to TRUE will try to use a direct calculation of the entropy from its definition and bypass the functions defined in the infotheo R package

Value

a matrix having as rownames and columnnames the attribute names from the input entity.attribute structure. The values are the mutual informations between the attributes in the region above the main diagonal. All the values below the diagonal are NA or zero.

Warning

Calculation of mutual information can be time consuming when many attributes are present for many entities

Author(s)

Adrian Pasculescu

References

Gibbons, F.D. and Roth F.P., (2002) Judging the Quality of Gene Expression-Based Clustering Methods Using Gene Annotation. Genome Research, vol. 12, pp1574-1581.

Cover,T.M. and Thomas,J.A. 1991. Elements of information theory (ed. D.L. Schilling). Wiley-Interscience,New York.

See Also

mi.GO.Yeast consolidate_entity_attribute

Examples

data(mi.GO.Yeast) ### is a precalculated example of mutual information for the Yeast genes 
                  ###   and their Gene Ontollogy (GO) attributes
str(mi.GO.Yeast)

#### the following example will generate the mutual information 
#### of 100 sampled pairs of Yeast , GO associations 
####    (otherwise it might take take minutes or hours to calculate the mutual information)
data(Yeast.GO.assocs) ### 
entity.attribute.sampled <- Yeast.GO.assocs[sample(1:nrow(Yeast.GO.assocs),100),]
mi.GO.Yeast.sampled <- attribute_mut_inf(entity.attribute.sampled, show.progress=TRUE)

pasculescu/ClusterJudge documentation built on May 29, 2019, 4:52 p.m.