read_annotation – prolfquapp

read annotation files

Description

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

library("prolfquapp")

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)

$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: 
    pattern_contaminants: NULL
    pattern_decoys: NULL
    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