rubin2wt.all: 2nd Rubin's rule Within-Variance Component (all peptides)

In mariechion/mi4p: Multiple Imputation for Proteomics

2nd Rubin's rule Within-Variance Component (all peptides)

Description

Computes the within-variance component in the 2nd Rubin's rule for all peptides.

Usage

rubin2wt.all(
  data,
  funcvar = mi4p::within_variance_comp_emmeans,
  metacond,
  is.parallel = FALSE,
  verbose = TRUE
)

Arguments

data	dataset
funcvar	function that should be used to compute the variance
metacond	a factor to specify the groups
is.parallel	should parallel computing be used?
verbose	should messages be displayed?

Value

List of variance-covariance matrices.

Author(s)

Frédéric Bertrand

References

M. Chion, Ch. Carapito and F. Bertrand (2021). Accounting for multiple imputation-induced variability for differential analysis in mass spectrometry-based label-free quantitative proteomics. \Sexpr[results=rd]{tools:::Rd_expr_doi("doi:10.1371/journal.pcbi.1010420")}.

Examples

library(mi4p)
data(datasim)
datasim_imp <- multi.impute(data = datasim[,-1], 
conditions = attr(datasim,"metadata")$Condition, method = "MLE")
rubin2wt.all(datasim_imp[1:5,,],funcvar = within_variance_comp_emmeans,
attr(datasim,"metadata")$Condition)

mariechion/mi4p documentation built on Oct. 3, 2024, 4:50 a.m.