analyze {autonomics} | R Documentation |
Analyze
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 )
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 |
SummarizedExperiment
require(magrittr) file <- download_data('atkin18.metabolon.xlsx') object <- read_metabolon(file, plot=FALSE) object %<>% analyze(pca=TRUE, subgroupvar = 'Group', fit='limma')