read_metabolon: Read metabolon xlsxfile

In bhagwataditya/autonomics: Unified statistal Modeling of Omics Data

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,
  groupvar = "Group",
  verbose = TRUE
)

read_metabolon(
  file,
  sheet = "OrigScale",
  fidvar = "BIOCHEMICAL",
  sidvar = "(CLIENT_IDENTIFIER|Client ID)",
  sfile = NULL,
  by.x = "sample_id",
  by.y = NULL,
  groupvar = "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 = as.formula(sprintf("~ %s", groupvar)),
  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
groupvar	string
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/autonomics documentation built on Nov. 1, 2024, 5:47 a.m.