Extract response column of a protein into matrix Median polish estimates of e.g. protein abundances for entire data.frame

Extract response column of a protein into matrix Median polish estimates of e.g. protein abundances for entire data.frame

Usage

medpolish_estimate_df(pdata, response, feature, sample_name)

Arguments

pdata

data.frame

response

column name with intensities

feature

column name e.g. peptide ids

sample_name

column name e.g. sample_name

Value

data.frame

See also

medpolish_estimate

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

Other plotting: ContrastsPlotter, INTERNAL_FUNCTIONS_BY_FAMILY, missigness_histogram(), missingness_per_condition(), missingness_per_condition_cumsum(), plot_estimate(), plot_heatmap(), plot_heatmap_cor(), plot_hierarchies_add_quantline(), plot_hierarchies_boxplot_df(), plot_hierarchies_line(), plot_hierarchies_line_df(), plot_intensity_distribution_violin(), plot_na_heatmap(), plot_pca(), plot_raster(), plot_sample_correlation(), upset_interaction_missing_stats(), upset_missing_stats()

Examples

bb <- sim_lfq_data_peptide_config(Nprot = 20)
#> creating sampleName from file_name column
#> completing cases
#> completing cases done
#> setup done
conf <- bb$config
data <- bb$data

conf$hierarchy_depth <- 1
xnested <- data |>
  dplyr::group_by(across(all_of(conf$hierarchy_keys_depth()))) |>
  tidyr::nest()

feature <- base::setdiff(
  conf$hierarchy_keys(),
  conf$hierarchy_keys_depth()
)
x <- xnested$data[[1]]
bb <- medpolish_estimate_df(x,
  response = conf$get_response(),
  feature = feature,
  sample_name = conf$sample_name
)
prolfqua:::.reestablish_condition(x, bb, conf$sample_name,
  conf$factor_keys(), conf$file_name, conf$isotope_label)
#> # A tibble: 12 × 5
#>    sampleName group_ sample  isotopeLabel medpolish
#>    <chr>      <chr>  <chr>   <chr>            <dbl>
#>  1 A_V1       A      A_V1    light             30.0
#>  2 A_V2       A      A_V2    light             29.8
#>  3 A_V3       A      A_V3    light             29.1
#>  4 A_V4       A      A_V4    light             29.9
#>  5 B_V1       B      B_V1    light             32.1
#>  6 B_V2       B      B_V2    light             32.4
#>  7 B_V3       B      B_V3    light             31.7
#>  8 B_V4       B      B_V4    light             33.5
#>  9 Ctrl_V1    Ctrl   Ctrl_V1 light             22.1
#> 10 Ctrl_V2    Ctrl   Ctrl_V2 light             18.5
#> 11 Ctrl_V3    Ctrl   Ctrl_V3 light             19.8
#> 12 Ctrl_V4    Ctrl   Ctrl_V4 light             21.4