However, there may be cases where an organisation’s security policies do not allow data to be uploaded to the web.
For this reason, the MetaboAnalyst website describes how to install the ‘MetaboAnalystR’ package, which allows similar analyses to be carried out in a local environment rather than on the web.
However, the method described causes an error when installing the ‘SSPA’ package. Information on how to solve this problem is not easy to find.
As a result, some people may want to use the MetaboAnalyst in their local environment, but find it difficult to implement.
Therefore, we will show you how to create the ‘MetaboAnalystR’ package, which is very useful if you have a specific analysis method in MetaboAnalyst, as even the R commands that MetaboAnalyst outputs can be routinely executed once you have them.
The example shows a new installation of R version 4.2.2.
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Preparation
The following is the preparation required to install the “MetaboAnalystR” package: Download and install RTools from the link provided for your version of R.
Next, download “SSPA_2.22.1.tar.gz” to your desktop from the link below. To download, click on the link next to “Source Package” at the bottom of the page.
This is an example of an analysis using “cow_diet.csv” data from “Analysis Path”, “Statistics [one factor]” and “Concentration Table” from the Data Format on the MetaboAnalyst website. and Biomarker Analysis” and “cow_diet.csv” data from the “Concentration Table”.