extract_ri: Extract experimental RI from NIST library

In QizhiSu/mspcompiler: Compile Mass Spectral Libraries from Various Sources

Extract experimental RI from NIST library

Description

extract_ri offers a way to extract experimental RI from the NIST library if you have it installed.

Usage

extract_ri(ri_dat, user_dbu)

Arguments

ri_dat	The "ri.dat" file in the installation path (e.g., "~/Programs/nist17/mssearch/nist_ri").
user_dbu	The "USER.DBU" file in the installation path (e.g., "~/Programs/nist17/mssearch/nist_ri")

Details

Once you have NIST library installed, there will be a "ri.dat" file in the installation path (e.g., "~/Programs/nist17/mssearch"). This file contains all experimental RI in the NIST library but it is not human readable. This function firstly convert the "ri.dat" file into a data.frame. However, it is tricky to link RI values in the cleaned RI table to compounds in the msp file. Providing that the "USER.DBU" file in the installation path (e.g., "~/Programs/nist17/mssearch") contains InChIKey of each compound in RI table, we can assign correspondent InChIKey to the RI table, but this file is not human readable. Therefore, this function secondly provides a way to clean the "USER.DBU" file and then assign correspondent InChIKey to the RI table.

Value

A data.frame containing experimental RI and InChIKey assigned.

QizhiSu/mspcompiler documentation built on May 7, 2024, 4:25 a.m.