peak.alignment: Peak Alignment for Multi-sample Analysis

In HuanLab/JPA:

Peak Alignment for Multi-sample Analysis

Description

Performs XCMS peak alignment for all level 1, 2, 3, and target features identified in multi-sample analysis.

Usage

peak.alignment(data, bw = 5, minfrac = 0.5, mzwid = 0.015, minsamp = 1, max = 100, quantitative.method = "maxo")

Arguments

data	"MSdata" object generated in previous steps.
bw	numeric(1) defining the bandwidth (standard deviation ot the smoothing kernel) to be used. Default = 5.
minfrac	numeric(1) defining the minimum fraction of samples in at least one sample group in which the peaks have to be present to be considered as a peak group (feature). Default = 0.5.
mzwid	numeric(1) defining the size of the overlapping slices in mz dimension. Default = 0.015.
minsamp	numeric(1) with the minimum number of samples in at least one sample group in which the peaks have to be detected to be considered a peak group (feature). Default = 1.
max	numeric(1) with the maximum number of peak groups to be identified in a single mz slice. Default = 100.
quantitative.method	Definition of feature intensity: either "maxo" for peak height or "into" for peak area.

Value

Returns aligned feature table with an additional column containing intensity values for each additional sample in multi-sample analysis. Note: features' level information will be lost at this point.

Author(s)

Sam Shen, Jian Guo, Tao Huan

Examples

library(IPA)
dir = "X:/Users/Sam_Shen/IPAtest_20210330/multiDDA"
featureTable <- peak.picking(dir = dir, mz.tol = 10, ppm=10, peakwidth=c(5,20), mzdiff = 0.01,
                             snthresh = 6, integrate = 1, prefilter = c(3,100), noise = 100)
featureTable <- find.level3features(data = MSdata)
featureTable <- peak.alignment(data = MSdata, bw = 5, minfrac = 0.5, mzwid = 0.015,
                               minsamp = 1, max = 100, quantitative.method = "maxo")

HuanLab/JPA documentation built on April 14, 2023, 12:53 p.m.