Mercurial > repos > recetox > recetox_aplcms_compute_clusters

comparison utils.R @ 2:ce00e1d03c31 draft

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planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 724ecb1b81ebd8a67488b8a9397177b2ff0357db
author recetox
date Wed, 24 May 2023 14:48:47 +0000
parents 092bbb03a217
children a054eae3123c
comparison
equal deleted inserted replaced
1:092bbb03a217 2:ce00e1d03c31
37 features <- lapply(files, arrow::read_parquet) 37 features <- lapply(files, arrow::read_parquet)
38 features <- lapply(features, tibble::as_tibble) 38 features <- lapply(features, tibble::as_tibble)
39 return(features) 39 return(features)
40 } 40 }
41 41
42 save_parquet_collection <- function(table, sample_names, subdir) { 42 save_parquet_collection <- function(feature_tables, sample_names, subdir) {
43 dir.create(subdir) 43 dir.create(subdir)
44 for (i in seq_len(length(table$feature_tables))) { 44 for (i in seq_len(length(feature_tables))) {
45 filename <- file.path(subdir, paste0(subdir, "_", sample_names[i], ".parquet")) 45 filename <- file.path(subdir, paste0(subdir, "_", sample_names[i], ".parquet"))
46 feature_table <- as.data.frame(table$feature_tables[[i]]) 46 feature_table <- as.data.frame(feature_tables[[i]])
47 feature_table <- save_sample_name(feature_table, sample_names[i]) 47 feature_table <- save_sample_name(feature_table, sample_names[i])
48 arrow::write_parquet(feature_table, filename) 48 arrow::write_parquet(feature_table, filename)
49 } 49 }
50 } 50 }
51 51
55 55
56 save_tolerances <- function(table, tol_file) { 56 save_tolerances <- function(table, tol_file) {
57 mz_tolerance <- c(table$mz_tol_relative) 57 mz_tolerance <- c(table$mz_tol_relative)
58 rt_tolerance <- c(table$rt_tol_relative) 58 rt_tolerance <- c(table$rt_tol_relative)
59 arrow::write_parquet(data.frame(mz_tolerance, rt_tolerance), tol_file) 59 arrow::write_parquet(data.frame(mz_tolerance, rt_tolerance), tol_file)
60 }
61
62 get_mz_tol <- function(tolerances) {
63 return(tolerances$mz_tolerance)
64 }
65
66 get_rt_tol <- function(tolerances) {
67 return(tolerances$rt_tolerance)
68 } 60 }
69 61
70 save_aligned_features <- function(aligned_features, metadata_file, rt_file, intensity_file) { 62 save_aligned_features <- function(aligned_features, metadata_file, rt_file, intensity_file) {
71 save_data_as_parquet_file(aligned_features$metadata, metadata_file) 63 save_data_as_parquet_file(aligned_features$metadata, metadata_file)
72 save_data_as_parquet_file(aligned_features$rt, rt_file) 64 save_data_as_parquet_file(aligned_features$rt, rt_file)