doppelgangR (version 1.0.2)

phenoDist: Calculate distance between two vectors, rows of one matrix/dataframe, or rows of two matrices/dataframes.

Description

This function does some simple looping to allow x and y to be various combinations of vectors and matrices/dataframes.

Usage

phenoDist(x, y = NULL, bins = 10, vectorDistFun = vectorWeightedDist, 
    ...)

Arguments

x

A vector, matrix or dataframe

y

NULL, a vector, matrix, or dataframe. If x is a vector, y must also be specified.

bins

discretize continuous fields in the specified number of bins

vectorDistFun

A function of two vectors that returns the distance between those vectors.

...

Extra arguments passed on to vectorDistFun

Value

• a matrix of distances between pairs of rows of x (if y is unspecified), or between all pairs of rows between x and y (if both are provided).

Examples

example("phenoFinder")

pdat1 <- pData(esets2[[1]])
pdat2 <- pData(esets2[[2]])

## Use phenoDist() to calculate a weighted distance matrix
distmat <- phenoDist(as.matrix(pdat1), as.matrix(pdat2))
## Note outliers with identical clinical data, these are probably the same patients:
graphics::boxplot(distmat)