read annotation files

Usage

read_annotation(dsf, repeated = TRUE, SAINT = FALSE, prefix = "G_", QC = FALSE)

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

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)
#> $atable
#> <AnalysisConfiguration>
#>   Public:
#>     annotation_vars: function () 
#>     bin_resp: 
#>     clone: function (deep = FALSE) 
#>     factorDepth: 1
#>     factor_keys: function () 
#>     factor_keys_depth: function () 
#>     factors: list
#>     fileName: file
#>     get_response: function () 
#>     hierarchy: list
#>     hierarchyDepth: 1
#>     hierarchyKeys: function (rev = FALSE) 
#>     hierarchy_keys: function (rev = FALSE) 
#>     hierarchy_keys_depth: function (names = TRUE) 
#>     hkeysDepth: function (names = TRUE) 
#>     id_required: function () 
#>     id_vars: function () 
#>     ident_Score: 
#>     ident_qValue: qValue
#>     initialize: function (analysisTableAnnotation = NULL, analysisParameter = NULL) 
#>     is_response_transformed: FALSE
#>     isotopeLabel: isotopeLabel
#>     min_peptides_protein: 2
#>     normValue: NULL
#>     nr_children: nr_children
#>     opt_mz: 
#>     opt_rt: 
#>     parameter: active binding
#>     pop_response: function () 
#>     sampleName: name
#>     sep: ~
#>     set_response: function (colName) 
#>     table: active binding
#>     value_vars: function () 
#>     workIntensity: NULL
#> 
#> $annot
#>     file name group
#> 1 a1.raw aa_1     a
#> 2 a2.raw ba_1     a
#> 3 a3.raw aa_2     b
#> 4 a4.raw ba_2     b
#>