calculateDistance {mia}R Documentation

Calculate sample distances with vegan

Description

Will be removed by Bioc 3.15

Usage

calculateDistance(x, FUN = stats::dist, ...)

## S4 method for signature 'ANY'
calculateDistance(x, FUN = stats::dist, ...)

## S4 method for signature 'SummarizedExperiment'
calculateDistance(
  x,
  FUN = stats::dist,
  abund_values = exprs_values,
  exprs_values = "counts",
  transposed = FALSE,
  ...
)

Arguments

x

a SummarizedExperiment object containing a tree.

FUN

a function for distance calculation. The function must expect the input matrix as its first argument. With rows as samples and columns as features.

...

other arguments passed onto FUN

abund_values

a single character value for specifying which assay to use for calculation.

exprs_values

a single character value for specifying which assay to use for calculation. (Use abund_values instead. exprs_values will be disabled.)

transposed

Logical scalar, is x transposed with cells in rows?

Details

calculateDistance calculates a distance matrix between samples. The type of distance calculated can be modified by setting FUN, which expects a function with a matrix input as its first argument.

Value

a sample-by-sample distance matrix, suitable for NMDS, etc.

Examples

# generate some example data
mat <- matrix(1:60, nrow = 6)
df <- DataFrame(n = c(1:6))
se <- SummarizedExperiment(assays = list(counts = mat),
                           rowData = df)
## Not run: 
calculateDistance(se)

## End(Not run)


[Package mia version 1.2.3 Index]