Mercurial > repos > recetox > recetox_xmsannotator_advanced

comparison utils.R @ 3:6b5dec818827 draft default tip

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planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox-xmsannotator commit bc3445f7c41271b0062c7674108f57708d08dd28
author recetox
date Thu, 30 May 2024 14:53:48 +0000
parents 2c6fa447f6a0
children
comparison
equal deleted inserted replaced
2:50ac7359ffe7 3:6b5dec818827
1 library(recetox.xmsannotator) 1 library(recetox.xmsannotator)
2 library(dplyr) 2 library(dplyr)
3 3
4 load_table <- function(filename, filetype) { 4 load_table <- function(filename, filetype) {
5 if (filename == "None") { 5 if (filename == "None") {
6 return(NULL) 6 return(NULL)
7 } 7 }
8 if (filetype == "csv") { 8 if (filetype == "csv") {
9 return(as.data.frame(read.csv(filename))) 9 return(as.data.frame(read.csv(filename)))
10 } else { 10 } else {
11 return(as.data.frame(arrow::read_parquet(filename))) 11 return(as.data.frame(arrow::read_parquet(filename)))
12 } 12 }
13 } 13 }
14 14
15 save_table <- function(table, filename, filetype) { 15 save_table <- function(table, filename, filetype) {
16 if (filetype == "csv") { 16 if (filetype == "csv") {
17 write.csv(table, filename, row.names = FALSE) 17 write.csv(table, filename, row.names = FALSE)
18 } else { 18 } else {
19 arrow::write_parquet(table, filename) 19 arrow::write_parquet(table, filename)
20 } 20 }
21 } 21 }
22 22
23 create_filter_by_adducts <- function(comma_separated_values) { 23 create_filter_by_adducts <- function(comma_separated_values) {
24 if (comma_separated_values == "None") { 24 if (comma_separated_values == "None") {
25 return(NA) 25 return(NA)
26 } 26 }
27 filter_by <- strsplit(trimws(comma_separated_values), ",")[[1]] 27 filter_by <- strsplit(trimws(comma_separated_values), ",")[[1]]
28 return(filter_by) 28 return(filter_by)
29 } 29 }
30 30
31 create_peak_table <- function(metadata_table, intensity_table) { 31 create_peak_table <- function(metadata_table, intensity_table) {
32 metadata_table <- select(metadata_table, id, mz, rt) 32 metadata_table <- select(metadata_table, id, mz, rt)
33 peak_table <- inner_join(metadata_table, intensity_table, by = "id") 33 peak_table <- inner_join(metadata_table, intensity_table, by = "id")
34 peak_table <- rename(peak_table, peak = id) 34 peak_table <- rename(peak_table, peak = id)
35 peak_table$peak <- as.integer(peak_table$peak) 35 peak_table$peak <- as.integer(peak_table$peak)
36 return(peak_table) 36 return(peak_table)
37 } 37 }