fit_limma {autonomics} | R Documentation |
Fit model and test for differential expression
fit_limma( object, subgroupvar = if ("subgroup" %in% svars(object)) "subgroup" else NULL, formula = default_formula(object, subgroupvar, "limma"), contrastdefs = contrast_coefs(object, formula), block = NULL, weightvar = if ("weights" %in% assayNames(object)) "weights" else NULL, verbose = TRUE, plot = FALSE ) fit_lm( object, subgroupvar = if ("subgroup" %in% svars(object)) "subgroup" else NULL, formula = default_formula(object, subgroupvar, fit = "lm"), block = NULL, weightvar = if ("weights" %in% assayNames(object)) "weights" else NULL, contrastdefs = NULL, verbose = TRUE, plot = FALSE ) fit_lme( object, subgroupvar = if ("subgroup" %in% svars(object)) "subgroup" else NULL, formula = default_formula(object, subgroupvar, fit = "lme"), block = NULL, weightvar = if ("weights" %in% assayNames(object)) "weights" else NULL, contrastdefs = NULL, verbose = TRUE, plot = FALSE ) fit_lmer( object, subgroupvar = if ("subgroup" %in% svars(object)) "subgroup" else NULL, formula = default_formula(object, subgroupvar, fit = "lmer"), block = NULL, weightvar = if ("weights" %in% assayNames(object)) "weights" else NULL, contrastdefs = NULL, verbose = TRUE, plot = FALSE ) fit_wilcoxon( object, subgroupvar = if ("subgroup" %in% svars(object)) "subgroup" else NULL, formula = default_formula(object, subgroupvar, fit = "wilcoxon"), contrastdefs = contrast_coefs(object, formula = formula), block = NULL, weightvar = NULL, verbose = TRUE, plot = FALSE )
object |
SummarizedExperiment |
subgroupvar |
subgroup variable |
formula |
modeling formula |
contrastdefs |
contrastdef vector / matrix / list
|
block |
block svar (or NULL) |
weightvar |
NULL or name of weight matrix in assays(object) |
verbose |
whether to msg |
plot |
whether to plot |
Updated SummarizedExperiment
require(magrittr) file <- download_data('atkin18.somascan.adat') object <- read_somascan(file, plot=FALSE) object %<>% fit_limma(subgroupvar = 'SampleGroup') object %<>% fit_lm( subgroupvar = 'SampleGroup') plot_venn(is_sig(object, contrast='t3-t2')) S4Vectors::metadata(object)$limma <- S4Vectors::metadata(object)$lm <- NULL object %<>% fit_limma( subgroupvar = 'SampleGroup', block = 'Subject_ID') object %<>% fit_wilcoxon(subgroupvar = 'SampleGroup', block = 'Subject_ID') # object %<>% fit_lme( subgroupvar = 'SampleGroup', block = 'Subject_ID') # object %<>% fit_lmer( subgroupvar = 'SampleGroup', block = 'Subject_ID') plot_venn(is_sig(object, contrast='t3-t2'))