is_sig {autonomics} | R Documentation |
Is significant?
is_sig( object, fit = intersect(names(metadata(object)), TESTS), contrast = if (is_scalar(fit)) colnames(metadata(object)[[fit]]) else 1, quantity = "fdr" )
object |
SummarizedExperiment |
fit |
subset of autonomics::TESTS |
contrast |
subset of colnames(metadata(object)[[fit]]) |
quantity |
value in dimnames(metadata(object)[[fit]])[3] |
matrix: -1 (downregulated), +1 (upregulatd), 0 (not fdr significant)
require(magrittr) file <- download_data('fukuda20.proteingroups.txt') object <- read_proteingroups(file, plot=FALSE) object %<>% fit_lm() object %<>% fit_limma() issig <- is_sig(object, fit = c('lm','limma'), contrast = 'Adult-X30dpt') plot_venn(issig)