frag4feature,purityA-method {msPurity}R Documentation

Assign precursor purity scored fragmentation spectra to XCMS features

Description

Assign fragmentation spectra (MS/MS) scored via msPurity package to features from an XCMS set object.

Allows the user to filter out spectra below a certain threshold for purity.

Usage

## S4 method for signature 'purityA'
frag4feature(pa, xset, ppm = 5, plim = 0,
  intense = TRUE, convert2RawRT = TRUE, create_db = FALSE,
  out_dir = ".", db_name = NA, grp_peaklist = NA)

Arguments

pa

object; purityA object

xset

object; XCMS object derived from the same files as the puritydf

ppm

numeric; ppm tolerance between precursor mz and feature mz

plim

numeric; min purity of precursor to be included

intense

boolean; If the most intense precursor or the centered precursor is used

convert2RawRT

boolean; If retention time correction has been used in XCMS set this to TRUE

create_db

boolean; SQLite database will be created of the results

out_dir

character; Path where database will be created

db_name

character; If create_db is TRUE, a custom database name can be used, default is a time stamp

grp_peaklist

dataframe [optional]; Can use any peak dataframe to add to databse. Still needs to be derived from the xset object though

Value

purityA object with slots for fragmentation-XCMS links

Examples


msmsPths <- list.files(system.file("extdata", "lcms", "mzML", package="msPurityData"), full.names = TRUE, pattern = "MSMS")
xset <- xcms::xcmsSet(msmsPths, nSlaves = 1)
xset <- xcms::group(xset)
xset <- xcms::retcor(xset)
xset <- xcms::group(xset)

pa  <- purityA(msmsPths, interpol = "linear")
pa <- frag4feature(pa, xset)


[Package msPurity version 1.8.1 Index]