From 037805622f8535d7715a99928c7a5dcdc00bf165 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Todor=20Kondi=C4=87?= <kontrapunkt@uclmail.net>
Date: Sat, 11 Mar 2023 13:06:37 +0100
Subject: [PATCH] Start adding structure for MS2 extraction.
---
R/api.R | 11 +++++++----
R/data-model.R | 10 +++++++++-
R/extraction.R | 18 +++++++++++++-----
3 files changed, 29 insertions(+), 10 deletions(-)
diff --git a/R/api.R b/R/api.R
index 5f541b5..f56b600 100644
--- a/R/api.R
+++ b/R/api.R
@@ -337,7 +337,8 @@ extr_data <-function(m) {
## Big ms1 chromatogram table.
cg1 = new_ms1_cgm_table()
-
+
+ cg2 = new_ms2_cgm_table()
for (fn in fine[,unique(file)]) {
@@ -356,21 +357,23 @@ extr_data <-function(m) {
## Extract MS1 chromatograms.
fncg1 = new_ms1_cgm_table()
-
fncg1 = extr_ms1_cgm(ms=ms,
isotab=isotab1,
qrt=F,
fncg1)
-
fncg1 = extr_ms1_cgm(ms=ms,
isotab=isotab2,
qrt=T,
fncg1)
-
cg1 = cg1[fncg1,.(precid,
rt,
intensity=i.intensity,
scan=i.scan)]
+
+ ## Extract MS2 chromatograms.
+ fnfd = as.data.table(fData(ms),keep.rownames="scan",key="scan")
+ fncg2 = extr_ms2_cgm(fnfd,fncg1)
+ 1+1
}
diff --git a/R/data-model.R b/R/data-model.R
index 4e136f0..3befa40 100644
--- a/R/data-model.R
+++ b/R/data-model.R
@@ -124,10 +124,18 @@ new_ms2_cgm_cat <- function() {
an = integer(0))
}
+new_ms2_cgm_table <- function() {
+ ## Varios rt-related MS2 data.
+ data.table(precid = integer(0),
+ ce = numeric(0),
+ an = integer(0),
+ rt = numeric(0))
+}
+
new_ms2_cgm_table <- function() {
## Creates a chromatogram.
data.table(precid = integer(0),
- an = intege r(0),
+ an = integer(0),
rt = numeric(0),
intensity = numeric(0),
scan = character(0),
diff --git a/R/extraction.R b/R/extraction.R
index 0410eec..08ba53d 100644
--- a/R/extraction.R
+++ b/R/extraction.R
@@ -620,7 +620,7 @@ create_fine_table <- function(m) {
"rt_min",
"rt_max",
"file"),
- keyby=c("file","isofine")]
+ keyby=c("file","precid")]
}
@@ -660,14 +660,14 @@ extr_ms1_cgm <- function(ms,isotab,qrt,res) {
## fill the data table.
for (i in 1L:nrow(mzrng)) {
rt = rtime(x[i,1])
- isofine = isotab[(i),isofine]
- chunk = data.table(isofine=isofine,
+ precid = isotab[(i),precid]
+ chunk = data.table(precid=precid,
rt=rt,
intensity=intensity(x[i,1]),
scan = names(rt),
- key = c("isofine","rt"))
+ key = c("precid","rt"))
- res = res[chunk,.(isofine,
+ res = res[chunk,.(precid,
rt,
intensity=i.intensity,
scan=i.scan)]
@@ -678,3 +678,11 @@ extr_ms1_cgm <- function(ms,isotab,qrt,res) {
}
+extr_ms2_cgm <- function(feat_table,one_file_cg1) {
+ ## Get scanIdx.
+
+ browser()
+ precs = feat_table[one_file_cg1,.(scan,scanIdx),on="scan"]
+
+
+}
--
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