read_metabolon: Read metabolon xlsxfile

View source: R/3.7_read_metabolon.R

.read_metabolonR Documentation

Read metabolon xlsxfile

Description

Read metabolon xlsxfile

Usage

.read_metabolon(
  file,
  sheet = "OrigScale",
  fidvar = "BIOCHEMICAL",
  sidvar = "(CLIENT_IDENTIFIER|Client ID)",
  sfile = NULL,
  by.x = "sample_id",
  by.y = NULL,
  subgroupvar = "Group",
  verbose = TRUE
)

read_metabolon(
  file,
  sheet = "OrigScale",
  fidvar = "BIOCHEMICAL",
  sidvar = "(CLIENT_IDENTIFIER|Client ID)",
  sfile = NULL,
  by.x = "sample_id",
  by.y = NULL,
  subgroupvar = "Group",
  fnamevar = "BIOCHEMICAL",
  kegg_pathways = FALSE,
  smiles = FALSE,
  impute = TRUE,
  plot = FALSE,
  pca = plot,
  pls = plot,
  label = "feature_id",
  fit = if (plot) "limma" else NULL,
  formula = ~subgroup,
  block = NULL,
  coefs = NULL,
  contrasts = NULL,
  palette = NULL,
  verbose = TRUE
)

Arguments

file

metabolon xlsx file

sheet

excel sheet (number or string)

fidvar

featureid var

sidvar

samplid var

sfile

sample file

by.x

'file' mergeby column

by.y

'sfile' mergeby column

subgroupvar

subgroup var

verbose

TRUE or FALSE

fnamevar

featurename fvar

kegg_pathways

TRUE or FALSE: add kegg pathways?

smiles

TRUE or FALSE: add smiles?

impute

TRUE or FALSE: impute group-specific NA values?

plot

TRUE or FALSE

pca

TRUE or FALSE

pls

TRUE or FALSE

label

fvar

fit

model engine: 'limma', 'lm', 'lme(r)', 'wilcoxon' or NULL

formula

model formula

block

model blockvar: string or NULL

coefs

model coefficients of interest: character vector or NULL

contrasts

coefficient contrasts of interest: character vector or NULL

palette

NULL or colorvector

Value

SummarizedExperiment

Examples

file <- system.file('extdata/atkin.metabolon.xlsx', package = 'autonomics')
read_metabolon(file, plot = TRUE, block = 'Subject')

bhagwataditya/importomics documentation built on July 11, 2024, 11:26 a.m.