Fix mixes 9-11

EuracBiomedicalResearch · Nov 21, 2024 · af4dc4b · af4dc4b
1 parent eae5b57
commit af4dc4b
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Showing 4 changed files with 67 additions and 53 deletions.
diff --git a/R/match-standards-chunks.R b/R/match-standards-chunks.R
@@ -282,15 +282,15 @@ fts$ion_relative_intensity <- feature_table[fts$feature_id, "mean_high"]
 fts$ion_relative_intensity <- fts$ion_relative_intensity /
     max(fts$ion_relative_intensity)
 fts$ion_adduct <- feature_table[fts$feature_id, "adduct"]
-fts$compound_id <- hmdb_id
+fts$compound_id <- std_dilution$HMDB[std_dilution$name == std]
 fts$polarity <- POLARITY
 idb <- insertIon(idb, fts, addColumns = TRUE)
 pandoc.table(fts, split.tables = Inf, style = "rmarkdown")
 rm(fts)
 
 ## ---- add-ms2-spectra ----
 ms2$original_spectrum_id <- spectraNames(ms2)
-ms2$compound_id <- hmdb_id
+ms2$compound_id <- std_dilution$HMDB[std_dilution$name == std]
 ms2$original_file <- basename(ms2$dataOrigin)
 ms2$collisionEnergy <- 20
 ms2$collisionEnergy[grep("CE30", ms2$original_file)] <- 30

diff --git a/match-standards-serum-mix09.Rmd b/match-standards-serum-mix09.Rmd
@@ -297,7 +297,7 @@ ms2$confidence <- c("low", "low")
 ```{r, add-ions, echo = FALSE, results = "asis"}
 ```
 
-```{r, add-ms2-spectra, echo = FALSE}
+```{r, add-ms2-spectra, echo = FALSE, results = "asis"}
 ```
 
 
@@ -372,7 +372,7 @@ ms2$confidence <- c("low")
 ```{r, add-ions, echo = FALSE, results = "asis"}
 ```
 
-```{r, add-ms2-spectra, echo = FALSE}
+```{r, add-ms2-spectra, echo = FALSE, results = "asis"}
 ```
 
 
@@ -457,7 +457,7 @@ ms2$confidence <- c("high")
 ```{r, add-ions, echo = FALSE, results = "asis"}
 ```
 
-```{r, add-ms2-spectra, echo = FALSE}
+```{r, add-ms2-spectra, echo = FALSE, results = "asis"}
 ```
 
 
@@ -580,7 +580,7 @@ ms2$confidence <- c("high", "high", "low", "low")
 ```{r, add-ions, echo = FALSE, results = "asis"}
 ```
 
-```{r, add-ms2-spectra, echo = FALSE}
+```{r, add-ms2-spectra, echo = FALSE, results = "asis"}
 ```
 
 
@@ -719,7 +719,7 @@ ms2$confidence <- c("low")
 ```{r, add-ions, echo = FALSE, results = "asis"}
 ```
 
-```{r, add-ms2-spectra, echo = FALSE}
+```{r, add-ms2-spectra, echo = FALSE, results = "asis"}
 ```
 
 
@@ -807,7 +807,7 @@ ms2$confidence <- c("low")
 ```{r, add-ions, echo = FALSE, results = "asis"}
 ```
 
-```{r, add-ms2-spectra, echo = FALSE}
+```{r, add-ms2-spectra, echo = FALSE, results = "asis"}
 ```
 
 
@@ -886,7 +886,7 @@ ms2$confidence <- c("low")
 ```{r, add-ions, echo = FALSE, results = "asis"}
 ```
 
-```{r, add-ms2-spectra, echo = FALSE}
+```{r, add-ms2-spectra, echo = FALSE, results = "asis"}
 ```
 
 
@@ -1009,7 +1009,7 @@ ms2$confidence <- c("low")
 ```{r, add-ions, echo = FALSE, results = "asis"}
 ```
 
-```{r, add-ms2-spectra, echo = FALSE}
+```{r, add-ms2-spectra, echo = FALSE, results = "asis"}
 ```
 
 
@@ -1094,7 +1094,7 @@ ms2$confidence <- c("low", "low", "high", "high")
 ```{r, add-ions, echo = FALSE, results = "asis"}
 ```
 
-```{r, add-ms2-spectra, echo = FALSE}
+```{r, add-ms2-spectra, echo = FALSE, results = "asis"}
 ```
 
 
@@ -1189,7 +1189,7 @@ ms2$confidence <- c("low")
 ```{r, add-ions, echo = FALSE, results = "asis"}
 ```
 
-```{r, add-ms2-spectra, echo = FALSE}
+```{r, add-ms2-spectra, echo = FALSE, results = "asis"}
 ```
 
 
@@ -1203,6 +1203,7 @@ POLARITY <- "NEG"
 data <- filterFile(data_all, which(data_all$polarity == POLARITY))
 hmdb <- hmdb_neg
 hmdb_nl <- hmdb_neg_nl
+csp@tolerance <- 0.01
 ```
 
 ```{r, preprocessing, eval = !file.exists(paste0(RDATA_PATH, "processed_data_", POLARITY, ".RData")), message = FALSE}
@@ -1329,7 +1330,7 @@ ms2$confidence <- c("high")
 ```{r, add-ions, echo = FALSE, results = "asis"}
 ```
 
-```{r, add-ms2-spectra, echo = FALSE}
+```{r, add-ms2-spectra, echo = FALSE, results = "asis"}
 ```
 
 
@@ -1396,7 +1397,7 @@ ms2$confidence <- c("high")
 ```{r, add-ions, echo = FALSE, results = "asis"}
 ```
 
-```{r, add-ms2-spectra, echo = FALSE}
+```{r, add-ms2-spectra, echo = FALSE, results = "asis"}
 ```
 
 
@@ -1474,7 +1475,7 @@ ms2$confidence <- c("high", "high", "low", "low")
 ```{r, add-ions, echo = FALSE, results = "asis"}
 ```
 
-```{r, add-ms2-spectra, echo = FALSE}
+```{r, add-ms2-spectra, echo = FALSE, results = "asis"}
 ```
 
 
@@ -1623,7 +1624,7 @@ ms2$confidence <- c("high", "high")
 ```{r, add-ions, echo = FALSE, results = "asis"}
 ```
 
-```{r, add-ms2-spectra, echo = FALSE}
+```{r, add-ms2-spectra, echo = FALSE, results = "asis"}
 ```
 
 
@@ -1707,7 +1708,7 @@ ms2$confidence <- c("low", "low", "high", "high", "high", "high",
 ```{r, add-ions, echo = FALSE, results = "asis"}
 ```
 
-```{r, add-ms2-spectra, echo = FALSE}
+```{r, add-ms2-spectra, echo = FALSE, results = "asis"}
 ```
 
 
@@ -1778,7 +1779,7 @@ ms2$confidence <- c("high")
 ```{r, add-ions, echo = FALSE, results = "asis"}
 ```
 
-```{r, add-ms2-spectra, echo = FALSE}
+```{r, add-ms2-spectra, echo = FALSE, results = "asis"}
 ```
 
 
@@ -1859,7 +1860,7 @@ ms2$confidence <- c("high", "high", "low", "low", "low")
 ```{r, add-ions, echo = FALSE, results = "asis"}
 ```
 
-```{r, add-ms2-spectra, echo = FALSE}
+```{r, add-ms2-spectra, echo = FALSE, results = "asis"}
 ```
 
 
@@ -1935,7 +1936,7 @@ ms2$confidence <- c("high")
 ```{r, add-ions, echo = FALSE, results = "asis"}
 ```
 
-```{r, add-ms2-spectra, echo = FALSE}
+```{r, add-ms2-spectra, echo = FALSE, results = "asis"}
 ```
 
 ### Pipecolic acid
@@ -2073,7 +2074,7 @@ ms2$confidence <- c("low", "low", "high", "high", "high", "high",
 ```{r, add-ions, echo = FALSE, results = "asis"}
 ```
 
-```{r, add-ms2-spectra, echo = FALSE}
+```{r, add-ms2-spectra, echo = FALSE, results = "asis"}
 ```
 
 
@@ -2083,6 +2084,11 @@ ms2$confidence <- c("low", "low", "high", "high", "high", "high",
 
 # Summary on the ion database
 
+Summarizing the content that was added to the `IonDb`.
+
+```{r, iondb-summary, echo = FALSE, results = "asis"}
+```
+
 # Session information
 
 The R version and packages used in this analysis are listed below.

diff --git a/match-standards-serum-mix10.Rmd b/match-standards-serum-mix10.Rmd
@@ -294,7 +294,7 @@ ms2$confidence <- c("high")
 ```{r, add-ions, echo = FALSE, results = "asis"}
 ```
 
-```{r, add-ms2-spectra, echo = FALSE}
+```{r, add-ms2-spectra, echo = FALSE, results = "asis"}
 ```
 
 ### Adenosine
@@ -379,7 +379,7 @@ ms2$confidence <- c("high", "high", "low", "low", "low", "low")
 ```{r, add-ions, echo = FALSE, results = "asis"}
 ```
 
-```{r, add-ms2-spectra, echo = FALSE}
+```{r, add-ms2-spectra, echo = FALSE, results = "asis"}
 ```
 
 
@@ -458,7 +458,7 @@ ms2$confidence <- c("low", "low", "high", "high")
 ```{r, add-ions, echo = FALSE, results = "asis"}
 ```
 
-```{r, add-ms2-spectra, echo = FALSE}
+```{r, add-ms2-spectra, echo = FALSE, results = "asis"}
 ```
 
 ### Citric Acid
@@ -616,7 +616,7 @@ ms2$confidence <- c("low", "low", "high", "high")
 ```{r, add-ions, echo = FALSE, results = "asis"}
 ```
 
-```{r, add-ms2-spectra, echo = FALSE}
+```{r, add-ms2-spectra, echo = FALSE, results = "asis"}
 ```
 
 
@@ -714,7 +714,7 @@ ms2$confidence <- c("low")
 ```{r, add-ions, echo = FALSE, results = "asis"}
 ```
 
-```{r, add-ms2-spectra, echo = FALSE}
+```{r, add-ms2-spectra, echo = FALSE, results = "asis"}
 ```
 
 ### Ribulose 5-Phosphate
@@ -810,7 +810,7 @@ ms2$confidence <- c("high", "high")
 ```{r, add-ions, echo = FALSE, results = "asis"}
 ```
 
-```{r, add-ms2-spectra, echo = FALSE}
+```{r, add-ms2-spectra, echo = FALSE, results = "asis"}
 ```
 
 
@@ -914,7 +914,7 @@ ms2$confidence <- c("high", "low", "high", "low", "low")
 ```{r, add-ions, echo = FALSE, results = "asis"}
 ```
 
-```{r, add-ms2-spectra, echo = FALSE}
+```{r, add-ms2-spectra, echo = FALSE, results = "asis"}
 ```
 
 
@@ -996,7 +996,7 @@ ms2$confidence <- c("high")
 ```{r, add-ions, echo = FALSE, results = "asis"}
 ```
 
-```{r, add-ms2-spectra, echo = FALSE}
+```{r, add-ms2-spectra, echo = FALSE, results = "asis"}
 ```
 
 
@@ -1166,7 +1166,7 @@ ms2$confidence <- c("low", "low", "high")
 ```{r, add-ions, echo = FALSE, results = "asis"}
 ```
 
-```{r, add-ms2-spectra, echo = FALSE}
+```{r, add-ms2-spectra, echo = FALSE, results = "asis"}
 ```
 
 ### L-Aspartic Acid
@@ -1237,7 +1237,7 @@ ms2$confidence <- c("high")
 ```{r, add-ions, echo = FALSE, results = "asis"}
 ```
 
-```{r, add-ms2-spectra, echo = FALSE}
+```{r, add-ms2-spectra, echo = FALSE, results = "asis"}
 ```
 
 ### Citric Acid
@@ -1309,7 +1309,7 @@ ms2$confidence <- c("high")
 ```{r, add-ions, echo = FALSE, results = "asis"}
 ```
 
-```{r, add-ms2-spectra, echo = FALSE}
+```{r, add-ms2-spectra, echo = FALSE, results = "asis"}
 ```
 
 
@@ -1390,7 +1390,7 @@ ms2$confidence <- c("low")
 ```{r, add-ions, echo = FALSE, results = "asis"}
 ```
 
-```{r, add-ms2-spectra, echo = FALSE}
+```{r, add-ms2-spectra, echo = FALSE, results = "asis"}
 ```
 
 ### Fumaric Acid
@@ -1469,7 +1469,7 @@ ms2$confidence <- c("low", "low")
 ```{r, add-ions, echo = FALSE, results = "asis"}
 ```
 
-```{r, add-ms2-spectra, echo = FALSE}
+```{r, add-ms2-spectra, echo = FALSE, results = "asis"}
 ```
 
 ### GDP
@@ -1619,7 +1619,7 @@ ms2$confidence <- c("low", "high", "high", "high", "high")
 ```{r, add-ions, echo = FALSE, results = "asis"}
 ```
 
-```{r, add-ms2-spectra, echo = FALSE}
+```{r, add-ms2-spectra, echo = FALSE, results = "asis"}
 ```
 
 
@@ -1697,7 +1697,7 @@ ms2$confidence <- c("low", "high")
 ```{r, add-ions, echo = FALSE, results = "asis"}
 ```
 
-```{r, add-ms2-spectra, echo = FALSE}
+```{r, add-ms2-spectra, echo = FALSE, results = "asis"}
 ```
 
 
@@ -1776,7 +1776,7 @@ ms2$confidence <- c("low", "low")
 ```{r, add-ions, echo = FALSE, results = "asis"}
 ```
 
-```{r, add-ms2-spectra, echo = FALSE}
+```{r, add-ms2-spectra, echo = FALSE, results = "asis"}
 ```
 
 
@@ -1857,7 +1857,7 @@ ms2$confidence <- c("low", "low")
 ```{r, add-ions, echo = FALSE, results = "asis"}
 ```
 
-```{r, add-ms2-spectra, echo = FALSE}
+```{r, add-ms2-spectra, echo = FALSE, results = "asis"}
 ```
 
 ## Standards without any matching feature
@@ -1868,6 +1868,9 @@ ms2$confidence <- c("low", "low")
 
 Summarizing the content that was added to the `IonDb`.
 
+```{r, iondb-summary, echo = FALSE, results = "asis"}
+```
+
 # Session information
 
 The R version and packages used in this analysis are listed below.