EMA (version 1.4.3)

clust.dist: Computes distances on a data matrix

Description

Computes distances between the columns of an expression matrix using the specified distance measure.

Usage

clust.dist(mat, meth.dis="euclidean")

Arguments

mat

Expression matrix, genes on rows and samples on columns

meth.dis

Character string specifying the distance measure to be used. This must be one of 'euclidean', 'manhattan', 'pearson', 'pearsonabs', 'spearman', 'spearmanabs', 'jaccard', 'dice'

Value

• A distance matrix.

Details

Available distance measures are (written for two vectors x and y):
• 'euclidean' : Usual square distance between the two vectors.
• 'manhattan' : Absolute distance between the two vectors
• 'pearson' : Pearson correlation distance. (1 - r)/2
• 'pearsonabs' : Absolute Pearson correlation distance. 1 - abs(r)
• 'spearman' : Spearman rank correlation distance. (1 - r)/2
• 'spearmanabs' : Absolute Spearlan rnak correlation distance. 1 - abs(r)
• 'jaccard' : Jaccard distance on 0-1 matrix
• 'dice': Dice distance on 0-1 matrix

See Also

jaccard,dice,daisy