make_volcano_dt: Create volcano datatable

In bhagwataditya/autonomics: Unified statistal Modeling of Omics Data

Create volcano datatable

Description

Create volcano datatable

Usage

make_volcano_dt(
  object,
  fit = fits(object)[1],
  coefs = default_coefs(object, fit = fit)[1],
  shape = "imputed",
  size = NULL,
  alpha = NULL,
  label = "feature_id"
)

Arguments

object	SummarizedExperiment
fit	'limma', 'lme', 'lm', 'wilcoxon'
coefs	character vector: coefs for which to plot volcanoes
shape	fvar or NULL
size	fvar or NULL
alpha	fvar or NULL
label	fvar or NULL

Value

data.table

Examples

file <- system.file('extdata/fukuda20.proteingroups.txt', package = 'autonomics')
object <- read_maxquant_proteingroups(file, impute = TRUE, fit = 'limma')
make_volcano_dt(object, fit = 'limma', coefs = 'Adult-X30dpt')

bhagwataditya/autonomics documentation built on Nov. 1, 2024, 5:47 a.m.