From 3f5e332dd5ba7eadbf84618fec56d03fdab00522 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Todor=20Kondi=C4=87?= <todor.kondic@uni.lu>
Date: Mon, 11 May 2020 08:07:12 +0200
Subject: [PATCH] extraction: Add centroided1, centroided
* R/extraction.R(centroided1,centroided): New functions.
---
DESCRIPTION | 1 +
R/extraction.R | 24 ++++++++++++++++++++++++
2 files changed, 25 insertions(+)
diff --git a/DESCRIPTION b/DESCRIPTION
index f63fdc9..5172b2b 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -63,6 +63,7 @@ Imports:
tools,
scales,
parallel,
+ future,
yaml,
mzR,
MSnbase,
diff --git a/R/extraction.R b/R/extraction.R
index 3f49abb..0fcd989 100644
--- a/R/extraction.R
+++ b/R/extraction.R
@@ -19,6 +19,30 @@ load_raw_data<-function(fn,mode="inMemory") {
}
+centroided1 <- function(ms) {
+ if (all(MSnbase::centroided(ms)) == T)
+ return(T) else {
+ state <- MSnbase::isCentroided(ms)
+ N <- length(state)
+ fls <-length(which(state == F))
+ if (fls/(1.*N) < 0.01) T else F
+ }
+
+}
+
+centroided <- function(msvec) {
+ if (is.vector(msvec)) {
+ f <- list()
+ for (i in 1:length(msvec)) {
+ f[[i]] <- future::future(centroided1(msvec[[i]]))
+ }
+ lapply(f, FUN = future::value)
+ } else {
+ centroided1(msvec)
+ }
+
+}
+
acq_mz<-function(tabFn) {
df<-read.csv(tabFn,
stringsAsFactors=F,
--
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