R: Calculate Theta

calculateTheta {propr} | R Documentation

## Calculate Theta

### 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.

[Package propr version 4.1.6 Index]