From 2c63c103de0c294a216f950fceaf9f74c9684bbe Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Todor=20Kondi=C4=87?= <todor.kondic@uni.lu>
Date: Mon, 27 Apr 2020 12:15:49 +0200
Subject: [PATCH] R/api.R: Add mk_mzml_tab function
R/api.R(mk_mzml_tab): This version is script compatible.
---
R/api.R | 35 +++++++++++++++++++++++++++++++----
1 file changed, 31 insertions(+), 4 deletions(-)
diff --git a/R/api.R b/R/api.R
index 107691b..cd803fa 100644
--- a/R/api.R
+++ b/R/api.R
@@ -24,6 +24,13 @@ run <- function(fn_conf) {
conf
}
+
+
+run_in_dir <- function(conf) {
+ conf
+}
+
+
read_conf <- function(fn_conf) {
assertthat::assert_that(file.exists(fn_conf),msg=paste("Unable to read the configuration file:", fn_conf))
conf <- yaml::yaml.load_file(fn_conf)
@@ -74,8 +81,28 @@ vrfy_conf <- function(conf) {
return(conf)
}
-run_in_dir <- function(conf) {
- conf
+mk_mzml_tab <- function(data) {
+ files <- unlist(data,recursive = T)
+ sets <- unique(names(data))
+ tags <- c()
+ for (s in sets) {
+ tags<-c(tags,names(data[[s]]))
+ }
+ tags<-unique(tags)
+ nr<-length(files)
+ z<-suppressWarnings(data.table::data.table(Files=character(nr),
+ mode=factor(levels = names(MODEMAP)),
+ set=factor(levels = sets),
+ tag=factor(levels= c(TAG_DEF,tags)),
+ stringsAsFactors = F))
+ z$Files <- files
+ i <- 1
+ for (s in names(data)) {
+ for (t in names(data[[s]])) {
+ z[i,"set"] <- s
+ z[i,"tag"]<-t
+ i<-i+1
+ }
+ }
+ z
}
-
-
--
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