From f0bfa95be2fbbb4e1cc5d2597ee59beab9a4bb0d Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Todor=20Kondi=C4=87?= <todor.kondic@uni.lu>
Date: Fri, 25 Sep 2020 14:34:22 +0200
Subject: [PATCH] Add top-level auto-prescreening function
* R/api.R (prescreen): New function. This exported funciton performs a
range of checks on the spectra in m$extr$ms and produces the initial
m$out$tab$ftab file table.
---
NAMESPACE | 1 +
R/api.R | 11 +++++++++++
2 files changed, 12 insertions(+)
diff --git a/NAMESPACE b/NAMESPACE
index 1529b55..88439a8 100644
--- a/NAMESPACE
+++ b/NAMESPACE
@@ -9,6 +9,7 @@ export(load_compound_input)
export(load_data_input)
export(load_inputs)
export(mk_comp_tab)
+export(prescreen)
export(run)
export(run_in_dir)
import(data.table)
diff --git a/R/api.R b/R/api.R
index b8a85b6..95b06ee 100644
--- a/R/api.R
+++ b/R/api.R
@@ -293,3 +293,14 @@ conf_trans <- function(conf) {
conf$prescreen <- conf_trans_pres(conf$prescreen)
conf
}
+
+##' @export
+prescreen <- function(m) {
+ ## Top-level auto prescreening function.
+ m$qa <- create_qa_table(m$extr$ms,m$conf$prescreen)
+ mms1 <- assess_ms1(m)
+ m <- assess_ms2(mms1)
+ fields <- c("Files","adduct","ID",QA_COLS)
+ m$out$tab$ftab <- merge(m$out$tab$comp,m$qa$ms[,..fields],by=c("Files","adduct","ID"))
+ m
+}
--
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