Mercurial > repos > recetox > recetox_xmsannotator_advanced
view utils.R @ 1:2c6fa447f6a0 draft
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox-xmsannotator commit 8547c5323747595eabbeed29039a1b2363491243
author | recetox |
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date | Thu, 20 Jul 2023 06:29:06 +0000 |
parents | cfd2e19f00a9 |
children | 6b5dec818827 |
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library(recetox.xmsannotator) library(dplyr) load_table <- function(filename, filetype) { if (filename == "None") { return(NULL) } if (filetype == "csv") { return(as.data.frame(read.csv(filename))) } else { return(as.data.frame(arrow::read_parquet(filename))) } } save_table <- function(table, filename, filetype) { if (filetype == "csv") { write.csv(table, filename, row.names = FALSE) } else { arrow::write_parquet(table, filename) } } create_filter_by_adducts <- function(comma_separated_values) { if (comma_separated_values == "None") { return(NA) } filter_by <- strsplit(trimws(comma_separated_values), ",")[[1]] return(filter_by) } create_peak_table <- function(metadata_table, intensity_table) { metadata_table <- select(metadata_table, id, mz, rt) peak_table <- inner_join(metadata_table, intensity_table, by = "id") peak_table <- rename(peak_table, peak = id) peak_table$peak <- as.integer(peak_table$peak) return(peak_table) }