expdesign_advise_lipidomics: expdesign_advise_lipidomics

In ShinyFabio/ADViSELipidomics: Shinyapp for the acquisition and the analysis of lipidomics data

expdesign_advise_lipidomics

Description

expdesign_advise_lipidomics is the function

Usage

expdesign_advise_lipidomics(
  out,
  design_vars = "",
  batch_vars = "",
  batch_type = "",
  batch_method = "",
  rep_mean = FALSE,
  file_contrast = "contrast_list_mod.txt"
)

Arguments

out	List. It is the result from the sumexp_advise_lipidomics function.
design_vars	Character vector, with the names of the variables from the target file, considered as conditions of comparison, related to replicates/samples. Default = "Product".
batch_vars	Character vector, with the names of the variables from the target file, considered as batch effects for the entire experiment. Default = "".
batch_type	Character string. Different methodologies to cope with the eventual presence of batch effects: "none", "remove", "fit". Default = "fit".
batch_method	Character string. Different methodologies to cope with the selection of batch_type = "fit". It can be "given" or "estimate". Default = "given".
rep_mean	Logical value. It is for the selection of the dataset with the replicates (FALSE) or the dataset with the samples (TRUE). Default = FALSE.
file_contrast	Character string. It is the name of the file with the list of the comparisons (contrasts) of interest. Default = "contrast_list.txt".

Details

This function generates the experimental design for the subsequent differential analysis. At first, it provides the linear model formula with the selected design variables, considering the eventual presence of batch effects. Then, after the generation of the experimental design, it reads a list of comparisons of interest (contrast list) and generates the contrast matrix for the next steps. In case of batch_type == "fit" and batch_method == "estimate", the selected methodology creates surrogate variables to be added to the design matrix. Further information on removing batch effects is in 'diffexp_advise_lipidomics" function.

Value

res: a list with results from the Summarized Experiment step, updated with the design matrix, the contrast matrix and the contrast vector (comparisons).

Note

Last change 17/12/2021

ShinyFabio/ADViSELipidomics documentation built on March 21, 2023, 7:30 a.m.