make_SummarizedExperiments: make_SummarizedExperiments(pheno = NULL, onlysamples = NULL,...
In johnmcculloch/JAMS_BW: Just A Microbiology System

View source: R/make_SummarizedExperiments.R

make_SummarizedExperiments

R Documentation

make_SummarizedExperiments(pheno = NULL, onlysamples = NULL, onlyanalyses = c("LKT", "Product", "ECNumber", "Pfam", "Interpro", "resfinder", "PRINTS", "GO"), minnumsampanalysis = NULL, minpropsampanalysis = 0.1, restricttoLKTs = NULL, stratify_functions_by_taxon = TRUE, add_TNF_data = FALSE, list.data = NULL, phenolabels = NULL, cdict = cdict, threads = 8)

Description

Makes a SummarizedExperiment object for every analysis that is possible to make given loaded jams files in list.data.

Usage

make_SummarizedExperiments(
  pheno = NULL,
  onlysamples = NULL,
  onlyanalyses = c("LKT", "Product", "ECNumber", "Pfam", "Interpro", "resfinder",
    "PRINTS", "GO"),
  minnumsampanalysis = NULL,
  minpropsampanalysis = 0.1,
  restricttoLKTs = NULL,
  stratify_functions_by_taxon = TRUE,
  add_TNF_data = FALSE,
  list.data = NULL,
  phenolabels = NULL,
  cdict = cdict,
  threads = 8
)

johnmcculloch/JAMS_BW documentation built on March 29, 2024, 7:56 p.m.