.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')

[Package autonomics version 1.1.7 Index]