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Self Correlation

Source: R/method-correlation.R
selfCorrelation-methods.Rd

This function returns correlation coefficients for variables in one AbundanceData object against itself. It generally serves as a convenience wrapper around veupathUtils::correlation, with the exception that it additionally supports sparcc.

Usage

# S4 method for AbundanceData
selfCorrelation(
  data,
  method = c("spearman", "pearson", "sparcc"),
  format = c("ComputeResult", "data.table"),
  verbose = c(TRUE, FALSE),
  proportionNonZeroThreshold = 0.5,
  varianceThreshold = 0,
  stdDevThreshold = 0
)

Arguments

data

An AbundanceData object

method

string defining the type of correlation to run. The currently supported values are 'spearman','pearson' and 'sparcc'

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

ComputeResult object