summarize_hierarchy: Summarize hierarchy counts

In wolski/prolfqua: Proteomics Label Free Quantification

Summarize hierarchy counts

Description

E.g compute number of peptides for each protein

Usage

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 <- prolfqua_data('data_ionstar')$filtered()
bb$config <- old2new(bb$config)
stopifnot(nrow(bb$data) == 25780)
configur <- bb$config$clone(deep=TRUE)
data <- bb$data

summarize_hierarchy(data, configur)
summarize_hierarchy(data, configur, factors = character())

summarize_hierarchy(data, configur,
 hierarchy = configur$table$hierarchy_keys_depth() )
summarize_hierarchy(data, configur,
 hierarchy = NULL, factors = configur$table$factor_keys_depth() )
configur$table$hierarchyDepth = 1
summarize_hierarchy(data, configur,
 factors = configur$table$factor_keys_depth())
configur$table$hierarchyDepth = 2
summarize_hierarchy(data, configur)
configur$table$hierarchyDepth = 3
summarize_hierarchy(data, configur )
configur$table$hierarchyDepth = 4
summarize_hierarchy(data, configur )

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