Summarizes the intensities within hierarchy

Summarizes the intensities within hierarchy

intensity_summary_by_hkeys(data, config, func)

Arguments

func

- a function working on a matrix of intensities for each protein.

Value

retuns function object

See also

Other aggregation: INTERNAL_FUNCTIONS_BY_FAMILY, aggregate_intensity_topN(), estimate_intensity(), medpolish_estimate(), medpolish_estimate_df(), medpolish_estimate_dfconfig(), medpolish_protein_estimates(), plot_estimate(), plot_hierarchies_add_quantline(), plot_hierarchies_line(), plot_hierarchies_line_df(), rlm_estimate(), rlm_estimate_dfconfig()

Other deprecated: INTERNAL_FUNCTIONS_BY_FAMILY, medpolish_protein_estimates()

Examples

bb <-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
data <- bb$data
config <- bb$config
x <- intensity_summary_by_hkeys(data, config, func = medpolish_estimate)
#> starting aggregation
res <- x("unnest")
res$data |> dim()
#> [1] 120   6


x <- intensity_summary_by_hkeys(data, config, func = medpolish_estimate)
#> starting aggregation
dd <- x(value = "plot")
stopifnot(nrow(dd) == length(unique(bb$data$protein_Id)))

dd$plot[[2]]
#> Warning: Removed 2 rows containing missing values or values outside the scale range
#> (`geom_point()`).
#> Warning: Removed 2 rows containing missing values or values outside the scale range
#> (`geom_point()`).


# example how to add peptide count information
tmp <- summarize_hierarchy(data, config)
tmp <- dplyr::inner_join(tmp, x("wide")$data, by = config$table$hierarchy_keys_depth())
tmp
#> # A tibble: 10 × 16
#>    protein_Id  isotopeLabel_n peptide_Id_n isotopeLabel  A_V1  A_V2  A_V3  A_V4
#>    <chr>                <int>        <int> <chr>        <dbl> <dbl> <dbl> <dbl>
#>  1 0EfVhX~0087              1            3 light         21.5  20.1  18.2  20.4
#>  2 7cbcrd~5725              1            1 light         30.4  30.4  29.6  27.8
#>  3 9VUkAq~4703              1            1 light         17.1  17.3  19.0  18.8
#>  4 BEJI92~5282              1            2 light         19.9  21.0  21.8  21.9
#>  5 CGzoYe~2147              1            1 light         24.1  24.2  25.0  23.8
#>  6 DoWup2~5896              1            1 light         24.2  24.4  23.3  23.4
#>  7 Fl4JiV~8625              1            4 light         20.6  20.6  20.7  20.2
#>  8 HvIpHG~9079              1            2 light         18.5  19.4  16.9  18.8
#>  9 JcKVfU~9653              1            7 light         29.8  30.4  29.2  32.0
#> 10 SGIVBl~5782              1            6 light         25.7  25.4  26.4  26.4
#> # ℹ 8 more variables: B_V1 <dbl>, B_V2 <dbl>, B_V3 <dbl>, B_V4 <dbl>,
#> #   Ctrl_V1 <dbl>, Ctrl_V2 <dbl>, Ctrl_V3 <dbl>, Ctrl_V4 <dbl>