read annotation files

Usage

read_annotation(
  dsf,
  repeated = TRUE,
  SAINT = FALSE,
  prefix = "G_",
  QC = FALSE,
  shorten_sample_names = TRUE,
  sample_name_suffix_length = 14L,
  sample_name_display_column = "sampleName"
)

Arguments

dsf: annotation table
repeated: is this a repeated measurement
SAINT: is this a SAINTexpress analysis
prefix: prefix for group levels
QC: if TRUE, read as QC annotation
shorten_sample_names: derive short display sample names from long names
sample_name_suffix_length: suffix length used for derived sample names
sample_name_display_column: preferred derived display sample-name column

Value

list with annot (annotation table), atable (analtysis table configuration), contrasts list with contrasts.

Examples

annot <- data.frame(
file = c("a1.raw","a2.raw","a3.raw","a4.raw"),
name = c("aa","ba","aa","ba"),
group = c("a","a","b","b"))
read_annotation(annot, QC = TRUE)
#> INFO [2026-06-23 20:43:00] Using derived sample display names in column 'sampleName'.
#> $atable
#> <AnalysisConfiguration>
#>   Public:
#>     annotation_vars: function () 
#>     bin_resp: 
#>     clone: function (deep = FALSE) 
#>     factor_depth: 1
#>     factor_keys: function () 
#>     factor_keys_depth: function () 
#>     factors: list
#>     file_name: file
#>     get_response: function () 
#>     hierarchy: list
#>     hierarchy_depth: 1
#>     hierarchy_keys: function (rev = FALSE) 
#>     hierarchy_keys_depth: function (names = TRUE) 
#>     id_required: function () 
#>     id_vars: function () 
#>     ident_q_value: qValue
#>     ident_score: 
#>     initialize: function () 
#>     is_response_transformed: FALSE
#>     isotope_label: isotopeLabel
#>     min_peptides_protein: 2
#>     norm_value: NULL
#>     nr_children: nr_children
#>     opt_mz: 
#>     opt_rt: 
#>     opt_se: 
#>     pop_response: function () 
#>     sample_name: sampleName
#>     sep: ~
#>     set_response: function (col_name) 
#>     value_vars: function () 
#>     work_intensity: NULL
#> 
#> $annot
#>     file name group sampleName
#> 1 a1.raw   aa     a         aa
#> 2 a2.raw   ba     a         ba
#> 3 a3.raw   aa     b       aa_1
#> 4 a4.raw   ba     b       ba_1
#>