is_sig {autonomics}R Documentation

Is significant?

Description

Is significant?

Usage

is_sig(
  object,
  fit = intersect(names(metadata(object)), TESTS),
  contrast = if (is_scalar(fit)) colnames(metadata(object)[[fit]]) else 1,
  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

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)

[Package autonomics version 1.2.0 Index]