Mercurial > repos > recetox > recetox_xmsannotator_advanced

comparison utils.R @ 5:a393c4383436 draft

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planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox-xmsannotator commit 1ab1a1dabfcebe11720de1411927a7438c1b64c1
author recetox
date Mon, 26 Jun 2023 13:55:44 +0000
parents
children d8766a6c08a4
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4:464c1e80a01f 5:a393c4383436
1 library(recetox.xmsannotator)
2 library(dplyr)
3
4 load_table <- function(filename, filetype) {
5 if (filename == "None") {
6 return(NULL)
7 }
8 if (filetype == "csv") {
9 return(as.data.frame(read.csv(filename)))
10 } else {
11 return(as.data.frame(arrow::read_parquet(filename)))
12 }
13 }
14
15 save_table <- function(table, filename, filetype) {
16 if (filetype == "csv") {
17 write.csv(table, filename, row.names = FALSE)
18 } else {
19 arrow::write_parquet(table, filename)
20 }
21 }
22
23 create_filter_by_adducts <- function(comma_separated_values) {
24 if (comma_separated_values == "None") {
25 return(NA)
26 }
27 filter_by <- strsplit(trimws(comma_separated_values), ",")[[1]]
28 return(filter_by)
29 }
30
31 create_peak_table <- function(metadata_table, intensity_table) {
32 metadata_table <- select(metadata_table, id, mz, rt)
33 peak_table <- inner_join(metadata_table, intensity_table, by = "id")
34 peak_table <- rename(peak_table, peak = id)
35 peak_table$peak <- as.integer(peak_table$peak)
36 return(peak_table)
37 }