.read_metabolon {autonomics}R Documentation

Read metabolon

Description

Read metabolon

Usage

.read_metabolon(
  file,
  sheet = "OrigScale",
  fid_var = "(COMP|COMP_ID)",
  sid_var = "(CLIENT_IDENTIFIER|Client ID)",
  sfile = NULL,
  sfileby = NULL,
  by = NULL,
  subgroupvar = "Group"
)

read_metabolon(
  file,
  sheet = "OrigScale",
  fid_var = "(COMP|COMP_ID)",
  sid_var = "(CLIENT_IDENTIFIER|Client ID)",
  sfile = NULL,
  sfileby = NULL,
  by = NULL,
  subgroupvar = "Group",
  fname_var = "BIOCHEMICAL",
  impute = FALSE,
  add_kegg_pathways = FALSE,
  add_smiles = FALSE,
  pca = FALSE,
  fit = NULL,
  formula = NULL,
  block = NULL,
  contrastdefs = NULL,
  verbose = TRUE,
  plot = TRUE
)

Arguments

file

metabolon xlsx filepath

sheet

xls sheet number or name

fid_var

feature_id fvar

sid_var

sampleid svar

sfile

sample file

sfileby

sample file mergeby column

by

metabolon file mergeby column

subgroupvar

subgroup svar

fname_var

featurename fvar

impute

whether to impute

add_kegg_pathways

whether to add kegg pathways

add_smiles

whether to add smiles

pca

whether to pca

fit

fit model: NULL, 'limma', 'lm', 'lme', 'lmer', 'wilcoxon'

formula

designmat formula

block

block svar

contrastdefs

contrastdef vector/matrix/list

verbose

whether to msg

plot

whether to plot

Value

SummarizedExperiment

Examples

file <- download_data('atkin18.metabolon.xlsx')
read_metabolon(file, pca = TRUE, fit = 'limma', block='SUB')

[Package autonomics version 1.2.0 Index]