constructPIS: Construct precursor ion scan data from multiple xcmsRaw...

In ohgane/ShotgunLipidomicsR: Utility Functions for Analysis/Visualization of ShotgunLipidomics Data.

Description

This function constructs a summrized data frame from a set of xcmsRaw objects. Currently, this is designed for use with LTQ-Orbitrap XL dataset acquired with "Parent ion mapping" method. With this method, no MS1 data was acquired and only MS2 data set was acquired over a range of m/z values. The data should be mzML converted from msConvert.

Usage

constructPIS(xrawlist, mz, mzabs = 0.5, ppm = NULL, digits = 1,
  centroid = TRUE, summarizeData = TRUE)

Arguments

xrawlist	A list of xcmsRaw objects to be used for construction of PIS data.
mz	A vector of m/z values of fragment ions.
mzabs	Window size for peak area calculation. Default, 0.5.
ppm	Window size for peak area calculation. If provided, this overrides mzabs setting.
digits	Digits used for fragment names.
centroid	Default, TRUE. For centroided data, this should be TRUE.
summarizeData	Default, TRUE. If set to FALSE, this function returns PIS data without averaging.

Value

A data frame containing PIS (precursor ion scanning) data set, with column names of mz, fragment, and int.

Examples

# Think about a situation where 1_PIS.mzML etc are present in a directory "mzML".
# input=list.files("../mzML", pattern="PIS", full.names=TRUE)
# xraw_list=lapply(input, xcmsRaw, includeMSn=TRUE, profstep=1)
# pisdata=constructPIS(xraw_list[1:3], mz=c(184.1, 208.1))
# xyplot(int~mz, groups=fragment, data=pisdata, type="l")

ohgane/ShotgunLipidomicsR documentation built on May 24, 2019, 11:55 a.m.