RODA is an R package for processing Raw Global Metabolomics Data Obtained from SCIEX 7500 or Similar Equipment. The package preprocessed the input data, run he data through a quality control pipeline and Then Run the data through Metaboloanalyst to Perform Statistical and Metabolic Pathway Enrichment Analysis
Check if R package "devtools" is installed.
# If not, install R package "devtools" first
install.packages("devtools")
Install RODA
devtools::install_github("Olamide025/RODA")
Or if you have the source file
install.packages("path/to/RODA_0.1.0.tar.gz", repos = NULL, type = "source")
make sure to replace "path/to/RODA_0.1.0.tar.gz" with the correct path to the tar.gz file on your local system
Input data are described below:
- Group_Info.txt (Identity of the various groups to which the individual samples belong)
- Internal_standards.txt (List of the internal standards used for the sample processing)
- Peak_Area.txt (Peak Intensity area for each of the sample as exported from SCIEX OS; samples on columns, metabolites on rows)
- Quality.txt (Quality of each of the peaks reported in the Peak_Area.txt file)
- RT.txt (Retension time of all the individual peaks of metabolites reported in Peak_Area.txt file)
- Normalization_Data.txt(normalization information for each sample which cold be cell number, protein amount etc)
Output: A dataframe of Filtered metabolites that pass quality check and that have been normalized based on user specified algorithm. The output is Metaboanlyst-Ready and can be feed directly into Metaboanalyst Pipeline. If the user wants, the output data will be feed into Metaboanalyst for pathway enrichment analysis and relevant plots will be generated for different pairing of samples of interest.
An example input data can also be found here
An examples work through can be found in an Rscript here