Mercurial > repos > recetox > recetox_aplcms_generate_feature_table
comparison utils.R @ 2:73d8537dcbd6 draft
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 724ecb1b81ebd8a67488b8a9397177b2ff0357db
| author | recetox |
|---|---|
| date | Wed, 24 May 2023 14:48:31 +0000 |
| parents | e8962c8340f4 |
| children | 477b5144a422 |
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| 1:e8962c8340f4 | 2:73d8537dcbd6 |
|---|---|
| 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) |