is_sig: Is significant?

In bhagwataditya/importomics: Unified Statistical Modeling of Omics Data

Is significant?

Description

Is significant?

Usage

is_sig(
  object,
  fit = fits(object)[1],
  contrast = coefs(object),
  quantity = "fdr"
)

Arguments

object	SummarizedExperiment
fit	subset of autonomics::TESTS
contrast	subset of colnames(metadata(object)[[fit]])
quantity	value in dimnames(metadata(object)[[fit]])[3]

Value

matrix: -1 (downregulated), +1 (upregulatd), 0 (not fdr significant)

Examples

file <- system.file('extdata/fukuda20.proteingroups.txt', package = 'autonomics')
object <- read_maxquant_proteingroups(file)
object %<>% fit_lm()
object %<>% fit_limma()
issig <- is_sig(object, fit = c('lm','limma'), contrast = 'Adult-X30dpt')
plot_contrast_venn(issig)

bhagwataditya/importomics documentation built on Nov. 28, 2024, 8:28 a.m.