.read_somascan {autonomics}

R Documentation

Read somascan

Description

Read data from somascan adat file

Usage

.read_somascan(
  file,
  fidvar = "SeqId",
  sidvar = "SampleId",
  sfile = NULL,
  sfileby = NULL,
  by = NULL,
  subgroupvar = "SampleGroup"
)

read_somascan(
  file,
  fidvar = "SeqId",
  sidvar = "SampleId",
  sfile = NULL,
  sfileby = NULL,
  by = NULL,
  subgroupvar = "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,
  pca = FALSE,
  fit = NULL,
  formula = NULL,
  block = NULL,
  contrastdefs = NULL,
  verbose = TRUE,
  plot = TRUE
)

Arguments

file	*.adat file path (string)
fidvar	featureid fvar (string)
sidvar	sampleid svar (string)
sfile	sample file
sfileby	sample file mergeby column
by	metabolon file mergeby column
subgroupvar	subgroup svar (string)
fname_var	featurename fvar (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	whether to rm NA svars
rm_single_value_svars	whether to rm single value svars
pca	whether to pca
fit	fit model: NULL, 'limma', 'lm', 'lme', 'lmer','wilcoxon'
formula	design formula (using svars)
block	block var
contrastdefs	contrastdef vector/matrix/list
verbose	whether to msg
plot	whether to plot

Value

Summarizedexperiment

Examples

file <- download_data('atkin18.somascan.adat')
read_somascan(file, pca = TRUE, fit = 'limma', block = 'Subject_ID')

---