From ca1026551cfe62eecf1e9e83e26ee0ae42181fc1 Mon Sep 17 00:00:00 2001
From: grlloyd
# load the packages
-library(MetMashR)
+library(MetMashR)
library(ggplot2)
library(structToolbox)
library(dplyr)
@@ -161,8 +161,8 @@ Importing the MTox700+ database
# show contents
.DT(df)
+ +# prepare workflow that uses MTox700+ as a source M = import_source() trim_whitespace( diff --git a/articles/index.html b/articles/index.html index c7e1d04..8058286 100644 --- a/articles/index.html +++ b/articles/index.html @@ -35,7 +35,7 @@
- - + diff --git a/articles/using_MetMashR.html b/articles/using_MetMashR.html index 707f630..ef63be4 100644 --- a/articles/using_MetMashR.html +++ b/articles/using_MetMashR.html @@ -55,7 +55,7 @@
@@ -273,8 +273,8 @@
Annotation Databases# show .DT(df)
Some annotation_database
objects also have a
+
Some annotation_database
objects also have a
write_database
method, that allows you to update the table
on disk. For example, in MetMashR
the rds_database
has a write_database
method.
@@ -530,8 +530,8 @@
An alternative to using rest_api
objects in every
+
An alternative to using rest_api
objects in every
workflow is to create separate workflow to generate a local database of
relevant data. This database can then be used in other workflows without
needing to query the api every time the workflow is run.
You can see that we obtained inchikey for more of the Lipids after +
+You can see that we obtained inchikey for more of the Lipids after normalising the lipid names.
MetMashR
also provides an interface to the
rgoslin
package to assist with Lipid annotations.
You can see that there is now a single record (row) for each +
+You can see that there is now a single record (row) for each LipidName, and that the multiple inchikeys associated with that LipidName have been collapsed into a single entry separated by semicolons.
diff --git a/authors.html b/authors.html index df949cd..b6d0bd7 100644 --- a/authors.html +++ b/authors.html @@ -35,7 +35,7 @@Lloyd GR, Weber RJM (2024). MetMashR: Metabolite Mashing with R. -R package version 0.1.0, https://computational-metabolomics.github.io/MetMashR/. +R package version 0.1.0, https://computational-metabolomics.github.io/MetMashR/.
@Manual{, title = {MetMashR: Metabolite Mashing with R}, diff --git a/index.html b/index.html index 937855f..1404aef 100644 --- a/index.html +++ b/index.html @@ -61,7 +61,7 @@
M = rds_database(tempfile())
df = read_database(M)
-#> Warning: cannot open compressed file '/tmp/RtmphgkKeU/file100c7ddf109', probable reason 'No such file or directory'
+#> Warning: cannot open compressed file '/tmp/RtmpEYRwVY/file100d2d423e63', probable reason 'No such file or directory'
#> Error in gzfile(file, "rb"): cannot open the connection