From c4fb344734b7872df5de5d4f432a236a197ece3d Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Todor=20Kondi=C4=87?= <todor.kondic@uni.lu>
Date: Tue, 12 May 2020 08:40:19 +0200
Subject: [PATCH] api: Add new phase mk_tol_funcs
* R/api.R(mk_tol_funcs): New function.
---
R/api.R | 31 +++++++++++++++++++++++++++++++
1 file changed, 31 insertions(+)
diff --git a/R/api.R b/R/api.R
index db9e935..dab4ab4 100644
--- a/R/api.R
+++ b/R/api.R
@@ -196,7 +196,38 @@ concurrency <- function(m) {
m
}
+mk_tol_funcs <- function(m) {
+ grab <- function(entry,unit) {
+ what <- paste0("\\<",unit,"\\>$")
+ entry <- trimws(entry,which="both")
+ if (grepl(what,entry))
+ as.numeric(sub(paste0("^(.*)",unit),"\\1",entry)) else NA_real_
+ }
+
+ asgn_mz_err <- function (entry, msg) {
+ eppm <- grab(entry,"ppm")
+ eda <- grab(entry,"Da")
+ shinyscreen:::assert(xor(is.na(eda), is.na(eppm)), msg = msg)
+ if (is.na(eda)) function(mz) eppm*1e-6*mz else function(mz) eda
+ }
+
+ asgn_t_err <- function (entry, msg) {
+ em <- grab(entry,"min")
+ es <- grab(entry,"s")
+ shinyscreen:::assert(xor(is.na(em), is.na(es)), msg = msg)
+ if (is.na(em)) es/60. else em
+
+
+ }
+ m$extr$tol$coarse <- asgn_mz_err(m$conf$tolerance[["ms1 coarse"]], msg = "ms1 coarse error: Only ppm, or Da units allowed.")
+ m$extr$tol$fine <- asgn_mz_err(m$conf$tolerance[["ms1 fine"]], msg = "ms1 fine error: Only ppm, or Da units allowed.")
+ m$extr$tol$eic <- asgn_mz_err(m$conf$tolerance$eic, msg = "eic error: Only ppm, or Da units allowed.")
+ m$extr$tol$rt <- asgn_t_err(m$conf$tolerance$rt, msg = "rt error: Only s(econds), or min(utes) allowed.")
+
+ m
+
+}
--
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