analyze {autonomics}R Documentation

Analyze

Description

Analyze

Usage

analyze(
  object,
  pca = FALSE,
  fit = NULL,
  subgroupvar = default_subgroupvar(object),
  formula = default_formula(object, subgroupvar, fit),
  block = NULL,
  weightvar = if ("weights" %in% assayNames(object)) "weights" else NULL,
  contrastdefs = contrast_coefs(object, formula),
  verbose = TRUE,
  plot = TRUE
)

Arguments

object

SummarizedExperiment

pca

whether to perform pca

fit

NULL, 'limma', 'lm', 'lme', 'lmer', or 'wilcoxon'

subgroupvar

subgroup svar

formula

model formula

block

block svar

weightvar

NULL or name of weight matrix in assays(object)

contrastdefs

contrastdefs vector/matrix/list

verbose

whether to msg

plot

whether to plot

Value

SummarizedExperiment

Examples

require(magrittr)
file <- download_data('atkin18.metabolon.xlsx')
object <- read_metabolon(file, plot=FALSE)
object %<>% analyze(pca=TRUE, subgroupvar = 'Group', fit='limma')

[Package autonomics version 1.2.0 Index]