delta_control-class: Control parameters for seaMass-Δ

In biospi/deamass: Statistical modelling for mass spectrometry omics

Control parameters for seaMass-Δ

Description

Define advanced control parameters for the seaMass-Σ Bayesian model.

Usage

delta_control(
  component.deviations = FALSE,
  keep = NULL,
  summarise = "groups",
  plot = c("group.quants.de", "component.deviations.de", "group.quants.de.batch",
    "component.deviations.de.batch"),
  model = "MCMCglmm",
  nwarmup = 4096,
  thin = 256,
  fdr.model = "ash",
  random.seed = 0
)

Arguments

component.deviations	Set this to TRUE to do differential expression analysis on the component deviations as weldeltl as the group quants.
keep	Outputs to keep MCMC samples for, NULL or a subset of c("markdown", "group.quants.de", "component.deviations.de")
summarise	Outputs to write csv summaries for, NULL or a subset of c("groups")
model	Either NULL (no differential expression analysis) or "MCMCglmm" (MCMCglmm differential expression analysis)
nwarmup	Number of MCMC warmup iterations to run for each chain with MCMCglmm differential expression analysis.
thin	MCMC thinning factor with MCMCglmm differential expression analysis.
fdr.model	Either NULL (no false discovery rate correction) or "ash" (ash false discovery rate correction)
random.seed	Random number seed
nthread	Number of CPU threads to employ

Functions

• delta_control: Generator function

biospi/deamass documentation built on May 20, 2023, 3:30 a.m.