README.md

In chunxuan98/NTAprioritization: What the Package Does (One Line, Title Case)

NTAprioritization

Summary

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: 1. getRTMSMS():return candidate list with MSMS macthing score(fragmentation score) > 0 and RT-MS/MS level 2. getTierlevel(): return data table in csv format with toxicity level and final priority in 5 tiers and another plot with highlighted tier 1 compounds.

Installation

NTAprioritization requires R version equal or newer than 4.1.1.

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("chunxuan98/NTAprioritization")

Data processing

1. 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

1. 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.

chunxuan98/NTAprioritization documentation built on April 12, 2022, 12:24 a.m.