medpolish_estimate_df: Median polish estimates of e.g. protein abundances for entire...

In wolski/prolfqua: Proteomics Label Free Quantification

Median polish estimates of e.g. protein abundances for entire data.frame

Description

Median polish estimates of e.g. protein abundances for entire data.frame

Usage

medpolish_estimate_df(pdata, response, feature, sampleName)

Arguments

pdata	data.frame
response	column name with intensities
feature	column name e.g. peptide ids
samples	column name e.g. sampleName

Value

data.frame

See Also

medpolish_estimate

Other aggregation: INTERNAL_FUNCTIONS_BY_FAMILY, aggregate_intensity_topN(), estimate_intensity(), intensity_summary_by_hkeys(), medpolish_estimate(), 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 plotting: ContrastsPlotter, INTERNAL_FUNCTIONS_BY_FAMILY, UpSet_interaction_missing_stats(), UpSet_missing_stats(), missigness_histogram(), missingness_per_condition(), missingness_per_condition_cumsum(), plot_NA_heatmap(), 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_pca(), plot_raster(), plot_sample_correlation(), plot_screeplot()

Examples

bb <- prolfqua_data('data_ionstar')$filtered()
bb$config <- old2new(bb$config)
stopifnot(nrow(bb$data) == 25780)
conf <- bb$config
data <- bb$data

conf$table$hierarchyDepth = 1
xnested <- data |>
  dplyr::group_by_at(conf$table$hierarchy_keys_depth()) |> tidyr::nest()

feature <- base::setdiff(conf$table$hierarchy_keys(),
  conf$table$hierarchy_keys_depth())
x <- xnested$data[[1]]
bb <- medpolish_estimate_df(x,
 response = conf$table$get_response(),
  feature = feature,
   sampleName = conf$table$sampleName)
prolfqua:::.reestablish_condition(x,bb, conf)

wolski/prolfqua documentation built on May 12, 2024, 10:16 p.m.