delta_control-class: Control parameters for seaMass-Δ

Description Usage Arguments Functions

Description

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

Usage

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delta_control(
  component.deviations = FALSE,
  keep = NULL,
  summarise = "groups",
  plot = c("group.quants.volcano", "group.quants.fdr", "group.quants.de"),
  model = "MCMCglmm",
  nwarmup = 4096,
  thin = 256,
  fdr.model = "ash",
  truth.func = NULL,
  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


biospi/deamass documentation built on Nov. 25, 2021, 1:18 p.m.