Summarize hierarchy counts

E.g compute number of peptides for each protein

summarize_hierarchy(
  pdata,
  config,
  hierarchy = config$table$hierarchy_keys_depth(),
  factors = character()
)

Arguments

pdata

data.frame

config

AnalysisConfiguration

hierarchy

for which hierarchy level (default up to hierarchy depth)

factors

which factors to include

See also

Other summary: INTERNAL_FUNCTIONS_BY_FAMILY, hierarchy_counts(), hierarchy_counts_sample(), nr_B_in_A_per_sample()

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$data
configur <- bb$config
summarize_hierarchy(data, configur)
#> # A tibble: 10 × 3
#>    protein_Id  isotopeLabel_n peptide_Id_n
#>    <chr>                <int>        <int>
#>  1 0EfVhX~0087              1            3
#>  2 7cbcrd~5725              1            1
#>  3 9VUkAq~4703              1            1
#>  4 BEJI92~5282              1            2
#>  5 CGzoYe~2147              1            1
#>  6 DoWup2~5896              1            1
#>  7 Fl4JiV~8625              1            4
#>  8 HvIpHG~9079              1            2
#>  9 JcKVfU~9653              1            7
#> 10 SGIVBl~5782              1            6
summarize_hierarchy(data, configur, factors = character())
#> # A tibble: 10 × 3
#>    protein_Id  isotopeLabel_n peptide_Id_n
#>    <chr>                <int>        <int>
#>  1 0EfVhX~0087              1            3
#>  2 7cbcrd~5725              1            1
#>  3 9VUkAq~4703              1            1
#>  4 BEJI92~5282              1            2
#>  5 CGzoYe~2147              1            1
#>  6 DoWup2~5896              1            1
#>  7 Fl4JiV~8625              1            4
#>  8 HvIpHG~9079              1            2
#>  9 JcKVfU~9653              1            7
#> 10 SGIVBl~5782              1            6

summarize_hierarchy(data, configur,
 hierarchy = configur$table$hierarchy_keys_depth() )
#> # A tibble: 10 × 3
#>    protein_Id  isotopeLabel_n peptide_Id_n
#>    <chr>                <int>        <int>
#>  1 0EfVhX~0087              1            3
#>  2 7cbcrd~5725              1            1
#>  3 9VUkAq~4703              1            1
#>  4 BEJI92~5282              1            2
#>  5 CGzoYe~2147              1            1
#>  6 DoWup2~5896              1            1
#>  7 Fl4JiV~8625              1            4
#>  8 HvIpHG~9079              1            2
#>  9 JcKVfU~9653              1            7
#> 10 SGIVBl~5782              1            6
summarize_hierarchy(data, configur,
 hierarchy = NULL, factors = configur$table$factor_keys_depth() )
#> # A tibble: 3 × 4
#>   group_ isotopeLabel_n protein_Id_n peptide_Id_n
#>   <chr>           <int>        <int>        <int>
#> 1 A                   1           10           28
#> 2 B                   1           10           28
#> 3 Ctrl                1           10           28
configur$table$hierarchyDepth = 1
summarize_hierarchy(data, configur,
 factors = configur$table$factor_keys_depth())
#> # A tibble: 30 × 4
#> # Groups:   group_ [3]
#>    group_ protein_Id  isotopeLabel_n peptide_Id_n
#>    <chr>  <chr>                <int>        <int>
#>  1 A      0EfVhX~0087              1            3
#>  2 A      7cbcrd~5725              1            1
#>  3 A      9VUkAq~4703              1            1
#>  4 A      BEJI92~5282              1            2
#>  5 A      CGzoYe~2147              1            1
#>  6 A      DoWup2~5896              1            1
#>  7 A      Fl4JiV~8625              1            4
#>  8 A      HvIpHG~9079              1            2
#>  9 A      JcKVfU~9653              1            7
#> 10 A      SGIVBl~5782              1            6
#> # ℹ 20 more rows
configur$table$hierarchyDepth = 2
summarize_hierarchy(data, configur)
#> # A tibble: 28 × 3
#> # Groups:   protein_Id [10]
#>    protein_Id  peptide_Id     n
#>    <chr>       <chr>      <int>
#>  1 0EfVhX~0087 ITLb4x1q       1
#>  2 0EfVhX~0087 ahQLlQY7       1
#>  3 0EfVhX~0087 dJkdz7so       1
#>  4 7cbcrd~5725 D5dQ4nKk       1
#>  5 9VUkAq~4703 eIC06D7g       1
#>  6 BEJI92~5282 HBkZvdhT       1
#>  7 BEJI92~5282 qQ1GK8Un       1
#>  8 CGzoYe~2147 mjHSHhoe       1
#>  9 DoWup2~5896 KVUnZ6oZ       1
#> 10 Fl4JiV~8625 GsUIOl6Q       1
#> # ℹ 18 more rows
configur$table$hierarchyDepth = 3
summarize_hierarchy(data, configur )
#> # A tibble: 28 × 3
#> # Groups:   protein_Id [10]
#>    protein_Id  peptide_Id     n
#>    <chr>       <chr>      <int>
#>  1 0EfVhX~0087 ITLb4x1q       1
#>  2 0EfVhX~0087 ahQLlQY7       1
#>  3 0EfVhX~0087 dJkdz7so       1
#>  4 7cbcrd~5725 D5dQ4nKk       1
#>  5 9VUkAq~4703 eIC06D7g       1
#>  6 BEJI92~5282 HBkZvdhT       1
#>  7 BEJI92~5282 qQ1GK8Un       1
#>  8 CGzoYe~2147 mjHSHhoe       1
#>  9 DoWup2~5896 KVUnZ6oZ       1
#> 10 Fl4JiV~8625 GsUIOl6Q       1
#> # ℹ 18 more rows
configur$table$hierarchyDepth = 4
summarize_hierarchy(data, configur )
#> # A tibble: 28 × 3
#> # Groups:   protein_Id [10]
#>    protein_Id  peptide_Id     n
#>    <chr>       <chr>      <int>
#>  1 0EfVhX~0087 ITLb4x1q       1
#>  2 0EfVhX~0087 ahQLlQY7       1
#>  3 0EfVhX~0087 dJkdz7so       1
#>  4 7cbcrd~5725 D5dQ4nKk       1
#>  5 9VUkAq~4703 eIC06D7g       1
#>  6 BEJI92~5282 HBkZvdhT       1
#>  7 BEJI92~5282 qQ1GK8Un       1
#>  8 CGzoYe~2147 mjHSHhoe       1
#>  9 DoWup2~5896 KVUnZ6oZ       1
#> 10 Fl4JiV~8625 GsUIOl6Q       1
#> # ℹ 18 more rows