sDistance: Function to compute the pairwise distance for a given data...

In supraHex: supraHex: a supra-hexagonal map for analysing tabular omics data

Description

sDistance is supposed to compute and return the distance matrix between the rows of a data matrix using a specified distance metric

Usage

sDistance(
data,
metric = c("pearson", "spearman", "kendall", "euclidean", "manhattan",
"cos", "mi",
"binary")
)

Arguments

data	a data frame or matrix of input data
metric	distance metric used to calculate a symmetric distance matrix. See 'Note' below for options available

Value

• dist: a symmetric distance matrix of nRow x nRow, where nRow is the number of rows of input data matrix

Note

The distance metrics are supported:

• "pearson": Pearson correlation. Note that two curves that have identical shape, but different magnitude will still have a correlation of 1

• "spearman": Spearman rank correlation. As a nonparametric version of the pearson correlation, it calculates the correlation between the ranks of the data values in the two vectors (more robust against outliers)

• "kendall": Kendall tau rank correlation. Compared to spearman rank correlation, it goes a step further by using only the relative ordering to calculate the correlation. For all pairs of data points (x_i, y_i) and (x_j, y_j), it calls a pair of points either as concordant (Nc in total) if (x_i - x_j)*(y_i - y_j)>0, or as discordant (Nd in total) if (x_i - x_j)*(y_i - y_j)<0. Finally, it calculates gamma coefficient (Nc-Nd)/(Nc+Nd) as a measure of association which is highly resistant to tied data

• "euclidean": Euclidean distance. Unlike the correlation-based distance measures, it takes the magnitude into account (input data should be suitably normalized

• "manhattan": Cityblock distance. The distance between two vectors is the sum of absolute value of their differences along any coordinate dimension

• "cos": Cosine similarity. As an uncentered version of pearson correlation, it is a measure of similarity between two vectors of an inner product space, i.e., measuring the cosine of the angle between them (using a dot product and magnitude)

• "mi": Mutual information (MI). MI provides a general measure of dependencies between variables, in particular, positive, negative and nonlinear correlations. The caclulation of MI is implemented via applying adaptive partitioning method for deriving equal-probability bins (i.e., each bin contains approximately the same number of data points). The number of bins is heuristically determined (the lower bound): 1+log2(n), where n is the length of the vector. Because MI increases with entropy, we normalize it to allow comparison of different pairwise clone similarities: 2*MI/[H(x)+H(y)], where H(x) and H(y) stand for the entropy for the vector x and y, respectively

• "binary": asymmetric binary (Jaccard distance index). the proportion of bits in which the only one divided by the at least one

See Also

sDmatCluster

Examples

# 1) generate an iid normal random matrix of 100x10 
data <- matrix( rnorm(100*10,mean=0,sd=1), nrow=100, ncol=10)

# 2) calculate distance matrix using different metric
sMap <- sPipeline(data=data)
# 2a) using "pearson" metric
dist <- sDistance(data=data, metric="pearson")
# 2b) using "cos" metric
# dist <- sDistance(data=data, metric="cos")
# 2c) using "spearman" metric
# dist <- sDistance(data=data, metric="spearman")
# 2d) using "kendall" metric
# dist <- sDistance(data=data, metric="kendall")
# 2e) using "euclidean" metric
# dist <- sDistance(data=data, metric="euclidean")
# 2f) using "manhattan" metric
# dist <- sDistance(data=data, metric="manhattan")
# 2g) using "mi" metric
# dist <- sDistance(data=data, metric="mi")
# 2h) using "binary" metric
# dist <- sDistance(data=data, metric="binary")

supraHex documentation built on Nov. 26, 2020, 2:01 a.m.