read_somascan: Read somascan adatfile

In bhagwataditya/autonomics: Unified Statistical Modeling of Omics Data

Read somascan adatfile

Description

Read somascan adatfile

Usage

.read_somascan(
  file,
  fidvar = "Target",
  sidvar = "SampleId",
  sfile = NULL,
  by.x = NULL,
  by.y = NULL,
  groupvar = "SampleGroup",
  verbose = TRUE
)

read_somascan(
  file,
  fidvar = "Target",
  sidvar = "SampleId",
  sfile = NULL,
  by.x = NULL,
  by.y = NULL,
  groupvar = "SampleGroup",
  fname_var = "EntrezGeneSymbol",
  sample_type = "Sample",
  feature_type = "Protein",
  sample_quality = c("FLAG", "PASS"),
  feature_quality = c("FLAG", "PASS"),
  rm_na_svars = FALSE,
  rm_single_value_svars = FALSE,
  plot = FALSE,
  label = "feature_id",
  pca = plot,
  pls = plot,
  fit = if (plot) "limma" else NULL,
  formula = as.formula(sprintf("~ %s", groupvar)),
  block = NULL,
  coefs = NULL,
  contrasts = NULL,
  palette = NULL,
  verbose = TRUE
)

Arguments

file	somascan (adat) file
fidvar	featureid var
sidvar	sampleid var
sfile	sample file
by.x	'file' mergeby column
by.y	'sfile' mergeby column
groupvar	string
verbose	TRUE or FALSE: message?
fname_var	featurename var: string
sample_type	subset of c('Sample','QC','Buffer','Calibrator')
feature_type	subset of c('Protein', 'Hybridization Control Elution','Rat Protein')
sample_quality	subset of c('PASS', 'FLAG', 'FAIL')
feature_quality	subset of c('PASS', 'FLAG', 'FAIL')
rm_na_svars	TRUE or FALSE: rm NA svars?
rm_single_value_svars	TRUE or FALSE: rm single value svars?
plot	TRUE or FALSE: plot ?
label	fvar
pca	TRUE or FALSE: run pca?
pls	TRUE or FALSE: run pls?
fit	model engine: 'limma', 'lm', 'lme(r)','wilcoxon' or NULL
formula	model formula
block	model blockvar
coefs	model coefficients of interest: character vector or NULL
contrasts	coefficient contrasts of interest: character vector or NULL
palette	character vector or NULL

Value

Summarizedexperiment

Examples

file <- system.file('extdata/atkin.somascan.adat', package = 'autonomics')
read_somascan(file, plot = TRUE, block = 'Subject')

bhagwataditya/autonomics documentation built on Dec. 1, 2024, 12:27 a.m.