correlation-AbundanceData-missing-method: Correlation of abundance data and metadata

In VEuPathDB/microbiomeComputations: Compute Results for Microbiome Analyses

Correlation of abundance data and metadata

Description

This function returns the correlation of all columns of an AbundanceData object with appropriate columns of a SampleMetadata object.

Usage

## S4 method for signature 'AbundanceData,missing'
correlation(
  data1,
  data2,
  method = c("spearman", "pearson"),
  format = c("ComputeResult", "data.table"),
  verbose = c(TRUE, FALSE),
  proportionNonZeroThreshold = 0.5,
  varianceThreshold = 0,
  stdDevThreshold = 0
)

Arguments

data1	AbundanceData object. Will correlate abundance variables with specified variables in data2
method	string defining the type of correlation to run. The currently supported values are 'spearman' and 'pearson'
format	string defining the desired format of the result. The currently supported values are 'data.table' and 'ComputeResult'.
verbose	boolean indicating if timed logging is desired
proportionNonZeroThreshold	numeric threshold to filter features by proportion of non-zero values across samples
varianceThreshold	numeric threshold to filter features by variance across samples
stdDevThreshold	numeric threshold to filter features by standard deviation across samples

Value

a ComputeResult object

VEuPathDB/microbiomeComputations documentation built on March 1, 2024, 7:21 a.m.