flagme (version 1.28.0)

calcTimeDiffs: Calculate retention time shifts from profile alignments

Description

This function takes the set of all pairwise profile alignments and use these to estimate retention time shifts between each pair of samples. These will then be used to normalize the retention time penalty of the signal peak alignment.

Usage

calcTimeDiffs(pd,ca.full,verbose=TRUE)

Arguments

pd

a peaksDataset object

ca.full

a clusterAlignment object, fit with

verbose

logical, whether to print out information

Value

list of same length as ca.full@alignments with the matrices giving the retention time penalties.

Details

Using the set of profile alignments,

References

Mark D Robinson (2008). Methods for the analysis of gas chromatography - mass spectrometry data PhD dissertation University of Melbourne.

See Also

peaksAlignment, clusterAlignment

Examples

require(gcspikelite)

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

# read data, peak detection results
pd <- peaksDataset(cdfFiles[1:2],mz=seq(50,550),rtrange=c(7.5,8.5))
pd <- addAMDISPeaks(pd,eluFiles[1:2])

# pairwise alignment using all scans
fullca <- clusterAlignment(pd, usePeaks=FALSE, df=100)

# calculate retention time shifts
timedf <- calcTimeDiffs(pd, fullca)