squeezeVarRob: Robustly Squeeze Sample Variances

In wolski/prolfqua: Proteomics Label Free Quantification

Robustly Squeeze Sample Variances

Description

This function squeezes a set of sample variances together by computing empirical Bayes posterior means in a way that is robust against the presence of very small non-integer degrees of freedom values.

Usage

squeezeVarRob(
  var,
  df,
  covariate = NULL,
  robust = FALSE,
  winsor.tail.p = c(0.05, 0.1),
  min_df = 1
)

Arguments

var	A numeric vector of independent sample variances.
df	A numeric vector of degrees of freedom for the sample variances.
covariate	If non-NULL, var.prior will depend on this numeric covariate. Otherwise, var.prior is constant.
robust	A logical indicating wheter the estimation of df.prior and var.prior should be robustified against outlier sample variances. Defaults to FALSE.
winsor.tail.p	A numeric vector of length 1 or 2, giving left and right tail proportions of x to Winsorize. Used only when robust=TRUE.
min_df	A numeric value indicating the minimal degrees of freedom that will be taken into account for calculating the prior degrees of freedom and prior variance.
k	A numeric value indicating that the calculation of the robust squeezed variances should Winsorize at k standard deviations.

Value

A list with components: var.post A numeric vector of posterior variances. var.prior The location of prior distribution. A vector if covariate is non-NULL, otherwise a scalar. df.prior The degrees of freedom of prior distribution. A vector if robust=TRUE, otherwise a scalar.

Examples

var <- rexp(1000)
df <- sample( 3:10, 1000, replace = TRUE)
tmp <- squeezeVarRob(var, df)
tmp <- squeezeVarRob(var, df, robust = TRUE)

wolski/prolfqua documentation built on May 12, 2024, 10:16 p.m.