calculateTheta: Calculate Theta

In propr: Calculating Proportionality Between Vectors of Compositional Data

Description

Calculate differential proportionality measure, theta. Used by propd to build the @results slot. A numeric alpha argument will trigger the Box-Cox transformation.

Usage

calculateTheta(counts, group, alpha = NA, lrv = NA, only = "all",
  weighted = FALSE, weights = as.matrix(NA))

Arguments

counts	A data.frame or matrix. A "count matrix" with subjects as rows and features as columns. Note that this matrix does not necessarily have to contain counts.
group	A character vector. Group or sub-group memberships, ordered according to the row names in counts.
alpha	A double. See vignette for details. Leave missing to skip Box-Cox transformation.
lrv	A numeric vector. A vector of pre-computed log-ratio variances. Optional parameter.
only	A character string. The name of the theta type to return if only calculating one theta type. Used to make updateCutoffs faster.
weighted	A boolean. Toggles whether to calculate theta using limma::voom weights.
weights	A matrix. Pre-computed limma-based weights. Optional parameter.

Value

A data.frame of theta values if only = "all". Otherwise, this function returns a numeric vector.

propr documentation built on Dec. 16, 2019, 9:30 a.m.