estimate_intensity: Aggregates e.g. protein abundances from peptide abundances

In wolski/prolfqua: Proteomics Label Free Quantification

Aggregates e.g. protein abundances from peptide abundances

Description

Aggregates e.g. protein abundances from peptide abundances

Usage

estimate_intensity(data, config, .func)

Arguments

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

Value

returns list with data (data.frame) and config (AnalysisConfiguration)

See Also

medpolish_estimate_dfconfig rlm_estimate_dfconfig

Other aggregation: INTERNAL_FUNCTIONS_BY_FAMILY, aggregate_intensity_topN(), intensity_summary_by_hkeys(), 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()

Examples

dd <- prolfqua::sim_lfq_data_peptide_config()
config <- dd$config
data <- dd$data
data <- prolfqua::transform_work_intensity(data, config, log2)
bbMed <- estimate_intensity(data, config, .func = medpolish_estimate_dfconfig)
bbRob <- estimate_intensity(data, config, .func = rlm_estimate_dfconfig)
nrow(bbMed$data)
nrow(bbRob$data)
length(bbMed$data$medpolish)
length(bbRob$data$lmrob)
xt <- dplyr::inner_join(bbMed$data, bbRob$data)
plot(xt$medpolish, xt$lmrob, log="xy", pch="*")
abline(0,1, col=2)

wolski/prolfqua documentation built on May 2, 2024, 7:23 p.m.