R/tidyMS_R6_TransitionCorrelations.R
normalize_log2_robscale.Rdnormalize data by log2 and robust scaling
normalize_log2_robscale(pdata, config)data.frame
AnalysisConfiguration
list with data.frame (data) and updated config (config)
Other preprocessing:
INTERNAL_FUNCTIONS_BY_FAMILY,
apply_to_response_matrix(),
filter_proteins_by_peptide_count(),
get_robscales(),
robust_scale(),
scale_with_subset(),
scale_with_subset_by_factors()
bb <- sim_lfq_data_peptide_config(Nprot = 100)
#> creating sampleName from fileName column
#> Warning: no nr_children column specified in the data, adding column nr_children and setting to 1.
#> completing cases
xx <- normalize_log2_robscale(bb$data, bb$config)
#> Column added : log2_abundance
#> Warning: Expected 2 pieces. Additional pieces discarded in 4200 rows [1, 2, 3, 4, 5, 6,
#> 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, ...].
#> Joining with `by = join_by(sampleName, protein_Id, peptide_Id)`
xx$config$table$workIntensity
#> [1] "abundance" "log2_abundance" "transformedIntensity"