correlationAlignment: Function for correlation-based alignment strategy of multiple GCMS samples

Description

Performs a correlation-based peak alignment of multiple GCMS peak lists; this function is able to align multiple samples, by a center-star strategy.

Usage

correlationAlignment(object, thr=0.85, D=20, penality=0.2, normalize=TRUE, minFilter=1)

Arguments

object

a peaksDataset object

thr

correlation trashold from 0 (min) to 1 (max)

retention time window in seconds

penality

the penality inflicted to a match between two peaks when the retention time difference exceed the parameter D

normalize

logical, whether to use normalized-to-100 peaks intensity or as such

minFilter

if a feature is matched in a number of samples less than minFilter, this feature is trashed. The value of minFilter must be smaller than the number of samples

Value

correlationAlignment object

Details

The correlation-based peak alignment for multiple GCMS peak lists uses a center-star tecnique to the alignment of the peaks. The combination of the D and penality parameters allow the users to force the algorithm to match the peaks close to the reference. The thr parameter control the matching factor.

Examples

Run this code

require(gcspikelite)

# paths and files
gcmsPath <- paste(find.package("gcspikelite"), "data", sep="/")
cdfFiles <- dir(gcmsPath,"CDF",full=TRUE)

# read data, peak detection results
pd <- peaksDataset(cdfFiles[1:2], mz=seq(50,550), rtrange=c(7.5,8.5))
pd <- addXCMSPeaks(files=cdfFiles[1:2], object=pd, peakPicking=c('mF'),
                   snthresh=3, fwhm=4, step=1, steps=2, mzdiff=0.5)
mp <- correlationAlignment(object=pd, thr=0.85, D=20, penality=0.2,
                           normalize=TRUE, minFilter=1)

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