Mercurial > repos > recetox > recetox_aplcms_unsupervised

comparison main.R @ 13:006736cab495 draft

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planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit b3e0c34f12c9c38fb34bf48197974620d60b50c5
author recetox
date Thu, 26 May 2022 16:44:17 +0000
parents 6057540f65a9
children 202ac259e077
comparison
equal deleted inserted replaced
12:6eeeebc35909 13:006736cab495
25 25
26 rcx_aplcms_to_rcx_xmsannotator <- function(peak_table) { 26 rcx_aplcms_to_rcx_xmsannotator <- function(peak_table) {
27 col_base <- c("feature", "mz", "rt") 27 col_base <- c("feature", "mz", "rt")
28 output_table <- peak_table %>% distinct(across(any_of(col_base))) 28 output_table <- peak_table %>% distinct(across(any_of(col_base)))
29 29
30 for (level in levels(peak_table$sample)) { 30 for (level in levels(factor(peak_table$sample))) {
31 subdata <- peak_table %>% 31 subdata <- peak_table %>%
32 filter(sample == level) %>% 32 filter(sample == level) %>%
33 select(any_of(c(col_base, "sample_intensity"))) %>% 33 select(any_of(c(col_base, "sample_intensity"))) %>%
34 rename(!!level := "sample_intensity") 34 rename(!!level := "sample_intensity")
35 output_table <- inner_join(output_table, subdata, by = col_base) 35 output_table <- inner_join(output_table, subdata, by = col_base)
99 save_all_corrected_features(res$corrected_features, sample_files) 99 save_all_corrected_features(res$corrected_features, sample_files)
100 100
101 save_aligned_feature_table(res$aligned_feature_sample_table, aligned_file) 101 save_aligned_feature_table(res$aligned_feature_sample_table, aligned_file)
102 save_recovered_feature_table(res$recovered_feature_sample_table, recovered_file, out_format) 102 save_recovered_feature_table(res$recovered_feature_sample_table, recovered_file, out_format)
103 } 103 }
104
105 two_step_hybrid_main <- function(sample_files, known_table_file, updated_known_table_file, recovered_file, aligned_file, out_format, metadata, ...) {
106 sample_files <- sort_samples_by_acquisition_number(sample_files)
107 metadata <- read.table(metadata, sep = ",", header = TRUE)
108
109 known_table <- read_known_table(known_table_file)
110 res <- two.step.hybrid(filenames = sample_files, known.table = known_table, work_dir = getwd(), metadata = metadata, ...)
111
112 save_known_table(res$known_table, updated_known_table_file)
113 save_aligned_feature_table(res$aligned_features, aligned_file)
114 save_recovered_feature_table(res$final_features, recovered_file, out_format)
115 }