Similarity-class {maDB}R Documentation

Class "Similarity"

Description

This class holds information about the similarity between a vector and another one (or the rows or columns of a numerical matrix). An instance of this class will be returned as the result of the dbSearchSimilarPattern function. So this object holds then information about the similarity (calculated with one of the different distance measurement functions (pearson, euclidian, spearman)) between a template gene pattern and a set of other gene expression or regulation patterns.

Objects from the Class

The function dbSearchSimilarPattern returns an instance of this class.

Slots

distances:
Object of class "numeric", this vector represents the distance (similarity) between numerical vectors.
distance.metric:
Object of class "character", the distance metric used to calculate the similarity.
data:
Object of class "matrix", the data matrix containing the values with which the template was compared.
template:
Object of class "numeric", the template vector.
template.id:
Object of class "character", the id of the template (if no custom template was used).

Methods

getData
signature(object = "Similarity"): returns the data matrix.
getDistances
signature(object = "Similarity"): returns the distances.
plot
signature(x = "Similarity"): plots the template and the 5 top matching vectors (see plotSimilarity for more options).
print
signature(x = "Similarity"): generic print function for the class Similarity.
sort
signature(x = "Similarity"): sorts the data ascending or descending according to the distance.

Author(s)

Johannes Rainer

See Also

dbSearchSimilarPattern plotSimilarity


[Package maDB version 1.2.0 Index]