converts LFQData object to SummarizedExperiment

For compatibility with Bioconductor

LFQDataToSummarizedExperiment(lfqdata)

Arguments

lfqdata: LFQData object

Value

SummarizedExperiment (bioconductor)

Examples


istar <- prolfqua::sim_lfq_data_peptide_config()
#> creating sampleName from fileName column
#> Warning: no nr_children column specified in the data, adding column nr_children and setting to 1.
#> completing cases
istar$config <- (istar$config)
data <- istar$data
lfqdata <- LFQData$new(data, istar$config)
lfqdata$to_wide()
#> $data
#> # A tibble: 28 × 15
#>    protein_Id  peptide_Id isotopeLabel  A_V1  A_V2  A_V3  A_V4  B_V1  B_V2  B_V3
#>    <chr>       <chr>      <chr>        <dbl> <dbl> <dbl> <dbl> <dbl> <dbl> <dbl>
#>  1 0EfVhX~0087 ITLb4x1q   light         19.4  NA    18.2  18.9  28.9  27.3  29.9
#>  2 0EfVhX~0087 ahQLlQY7   light         26.9  25.2  26.1  25.2  26.1  26.2  24.5
#>  3 0EfVhX~0087 dJkdz7so   light         NA    16.1  14.7  NA    25.7  23.9  25.5
#>  4 7cbcrd~5725 D5dQ4nKk   light         30.4  30.4  29.6  27.8  NA    21.6  20.9
#>  5 9VUkAq~4703 eIC06D7g   light         17.1  17.3  19.0  18.8  16.4  NA    17.4
#>  6 BEJI92~5282 HBkZvdhT   light         18.1  17.9  NA    NA    19.1  19.2  18.7
#>  7 BEJI92~5282 qQ1GK8Un   light         21.7  24.0  24.7  24.8  28.6  25.8  26.2
#>  8 CGzoYe~2147 mjHSHhoe   light         24.1  24.2  25.0  23.8  NA    31.3  31.1
#>  9 DoWup2~5896 KVUnZ6oZ   light         24.2  24.4  23.3  23.4  18.4  18.5  18.4
#> 10 Fl4JiV~8625 GsUIOl6Q   light         20.2  20.1  20.3  NA    25.0  25.5  24.9
#> # ℹ 18 more rows
#> # ℹ 5 more variables: B_V4 <dbl>, Ctrl_V1 <dbl>, Ctrl_V2 <dbl>, Ctrl_V3 <dbl>,
#> #   Ctrl_V4 <dbl>
#> 
#> $annotation
#> # A tibble: 12 × 4
#>    sampleName sample  group_ isotopeLabel
#>    <chr>      <chr>   <chr>  <chr>       
#>  1 A_V1       A_V1    A      light       
#>  2 A_V2       A_V2    A      light       
#>  3 A_V3       A_V3    A      light       
#>  4 A_V4       A_V4    A      light       
#>  5 B_V1       B_V1    B      light       
#>  6 B_V2       B_V2    B      light       
#>  7 B_V3       B_V3    B      light       
#>  8 B_V4       B_V4    B      light       
#>  9 Ctrl_V1    Ctrl_V1 Ctrl   light       
#> 10 Ctrl_V2    Ctrl_V2 Ctrl   light       
#> 11 Ctrl_V3    Ctrl_V3 Ctrl   light       
#> 12 Ctrl_V4    Ctrl_V4 Ctrl   light       
#> 
#> $rowdata
#> # A tibble: 28 × 3
#>    protein_Id  peptide_Id isotopeLabel
#>    <chr>       <chr>      <chr>       
#>  1 0EfVhX~0087 ITLb4x1q   light       
#>  2 0EfVhX~0087 ahQLlQY7   light       
#>  3 0EfVhX~0087 dJkdz7so   light       
#>  4 7cbcrd~5725 D5dQ4nKk   light       
#>  5 9VUkAq~4703 eIC06D7g   light       
#>  6 BEJI92~5282 HBkZvdhT   light       
#>  7 BEJI92~5282 qQ1GK8Un   light       
#>  8 CGzoYe~2147 mjHSHhoe   light       
#>  9 DoWup2~5896 KVUnZ6oZ   light       
#> 10 Fl4JiV~8625 GsUIOl6Q   light       
#> # ℹ 18 more rows
#> 
#> $config
#> <AnalysisConfiguration>
#>   Public:
#>     clone: function (deep = FALSE) 
#>     initialize: function (analysisTableAnnotation, analysisParameter = AnalysisParameters$new()) 
#>     parameter: AnalysisParameters, R6
#>     sep: ~
#>     table: AnalysisTableAnnotation, R6
#> 
if(require("SummarizedExperiment")){
   tmp <- LFQDataToSummarizedExperiment(lfqdata)
}

Arguments

Value

See also

Examples