expectedDistance: Calculate the expected values of distances between samples,...
In ALDEx2: Analysis Of Differential Abundance Taking Sample Variation Into Account

Description Usage Arguments Details Value References See Also Examples

Calculates the expected value of distances between samples, given an aldex Object, using the median value of distances derived from n Monte-Carlo replicates.

1 2	## S3 method for class 'expectedDistance' aldex(clrData)

clrData

an object of class aldex produced by the aldex function

Generates a distance matrix for each Monte-Carlo instance in an aldex Object. Calculates the median distance value across all instances.

Returns a dist Object.

Please use the citation given by citation(package="ALDEx").

aldex, aldex.clr dist

    data(selex)
        #subset for efficiency
        selex <- selex[1201:1600,]
    conds <- c(rep("NS", 7), rep("S", 7))
    x <- aldex.clr(selex, conds, mc.samples = 128, denom = "all", verbose = FALSE)
    x.dist <- aldex.expectedDistance(x)