NTAprioritization is an R package for analyzing raw candidate list obtained from non-target analysis. The raw candidate list can be obtained by pre-processing in Waters Porgenesis QI after acquisition by Waters LC-MS-QTOF. NTA prioritization enables a complete workflow from raw feature lists to a final prioritized identification list with multiple filters. The workflow starts with three parameters: spectral library searching scores, predicted retention time, and toxicity data. It includes 2 functions:
- getRTMSMS():return candidate list with MSMS macthing score(fragmentation score) > 0 and RT-MS/MS level
- getTierlevel(): return data table in csv format with toxicity level and final priority in 5 tiers and another plot with highlighted tier 1 compounds.
NTAprioritizationrequires R version equal or newer than 4.1.1. The following script allows to install rexposome dependencies:
if (!requireNamespace("BiocManager", quietly=TRUE)){ install.packages("BiocManager")}
packages = c('rcdk','rcdklibs','randomForest','leaps','caret','corrplot','tidyverse', 'mlr','dplyr','Metrics','ggpubr','ggplot2','miceadds','rio','openxlsx','ggrepel')
for( pkg in packages ) { if( !pkg %in% rownames( installed.packages() ) ) { message( "Installing ", pkg ) BiocManager::install( pkg )} }
- To install the package using:
(1)Download the packages to local folder (path_to_file)
install.packages(path_to_file, repos = NULL, type="source")
(2) The package can be installed using the R package devtools. devtools can be installed win the following code:
install.packages("devtools")
devtools::install_github("YANGJJ93MS/NTAprioritization")
- Get predicted retention time and RT-MS/MS level by typing getRTMSMS() in Rstudio console:
getRTMSMS()
interface pops up and direct to the source raw data in csv format
- Get Toxicity level and Compound priority in 5 tiers by typing getRTMSMS() in Rstudio console:
getTierlevel()
refer to the folder where the raw data is stored and find the result table and plot.
#new updates on the way