From 4262e53b4c5d1786cbb71b724e93ba63782896d4 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Todor=20Kondi=C4=87?= <kontrapunkt@uclmail.net>
Date: Wed, 29 Mar 2023 16:35:58 +0200
Subject: [PATCH] Move gen_summ from mix to data-model.
---
R/data-model.R | 16 ++++++++++++++++
R/mix.R | 14 --------------
2 files changed, 16 insertions(+), 14 deletions(-)
diff --git a/R/data-model.R b/R/data-model.R
index 79f177d..331b146 100644
--- a/R/data-model.R
+++ b/R/data-model.R
@@ -113,3 +113,19 @@ empty_spectra_table <- function() {
setkey(r,precid,scan)
r
}
+
+
+## Based on the `comprehensive' and `qa' tabs, greate `summ'.
+gen_summ <- function(comp,qa) {
+ comp_cols <- intersect(SUMM_COLS,colnames(comp))
+ rdcomp <- comp[,..comp_cols]
+ data.table::setkeyv(rdcomp,BASE_KEY)
+ summ <- qa[rdcomp,nomatch=F] #We changed `nomatch' cases from NA
+ #to F, because NA does not work well
+ #with X == F condition.
+ ## flgs <- c(QA_FLAGS,"ms2_sel")
+ ## summ[is.na(qa_ms1_exists),(flgs):=F]
+ data.table::setkeyv(summ,SUMM_KEY)
+ summ[.(F),c("qlt_ms1","qlt_ms2"):=0.,on="qa_ms1_exists"]
+ summ
+}
diff --git a/R/mix.R b/R/mix.R
index d0dc255..105b025 100644
--- a/R/mix.R
+++ b/R/mix.R
@@ -797,20 +797,6 @@ analyse_extracted_data_old <- function(extr,prescreen_param) {
res
}
-## Based on the `comprehensive' and `qa' tabs, greate `summ'.
-gen_summ <- function(comp,qa) {
- comp_cols <- intersect(SUMM_COLS,colnames(comp))
- rdcomp <- comp[,..comp_cols]
- data.table::setkeyv(rdcomp,BASE_KEY)
- summ <- qa[rdcomp,nomatch=F] #We changed `nomatch' cases from NA
- #to F, because NA does not work well
- #with X == F condition.
- ## flgs <- c(QA_FLAGS,"ms2_sel")
- ## summ[is.na(qa_ms1_exists),(flgs):=F]
- data.table::setkeyv(summ,SUMM_KEY)
- summ[.(F),c("qlt_ms1","qlt_ms2"):=0.,on="qa_ms1_exists"]
- summ
-}
--
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