annotateCleanMSMS: Annotate Cleaned MSMS

In schymane/GenFormR: Use GenForm for Formula Generation and MS/MS Annotation in R

Description

This takes the output from RunGenForm and creates a peaklist with the annotations for further use.

Usage

annotateCleanMSMS(cleanMSMS, GenForm_an_out, GenForm_loss_out, lowestPpm=TRUE, round=TRUE,
removeAnnoSpace=FALSE)

Arguments

cleanMSMS	File name for Cleaned MSMS text file output from RunGenForm
GenForm_an_out	File name for annotated MSMS text file output from RunGenForm
GenForm_loss_out	File name for annotated "loss" MSMS text file output from RunGenForm
lowestPpm	If TRUE, choses the lowest ppm subformula for assignment of formula to fragments. If FALSE, takes the first formula.
round	If TRUE, rounds the output to 4 (mz) and 1 (Int) decimal places for aesthetics. If FALSE, no rounding is done.
removeAnnoSpace	If TRUE, removes the space in the "no loss" annotation.

Value

Returns annotated peaks for further use

Author(s)

Emma Schymanski ([e-mail])

schymane/GenFormR documentation built on May 25, 2019, 8:32 p.m.