peaksAlignment-class {flagme}R Documentation

Data Structure for pairwise alignment of 2 GCMS samples

Description

Store the raw data and optionally, information regarding signal peaks for a number of GCMS runs

Usage

peaksAlignment(d1,d2,t1,t2,gap=.5,D=1000,timedf=NULL,df=30,verbose=TRUE,usePeaks=TRUE,compress=TRUE)

Arguments

d1 matrix of MS intensities for 1st sample (if doing a peak alignment, this contains peak apexes/areas; if doing a profile alignment, this contains scan intensities. Rows are m/z bins, columns are peaks/scans.
d2 matrix of MS intensities for 2nd sample
t1 vector of retention times for 1st sample
t2 vector of retention times for 2nd sample
gap gap penalty for dynamic programming algorithm
D time penalty (on same scale as retention time differences, t1 and t2)
timedf list (length = the number of pairwise alignments) of matrices giving the expected time differences expected at each pair of peaks (used with usePeaks=TRUE.
df integer, how far from the diagonal to go to calculate the similarity of peaks. Smaller value should run faster, but be careful not to choose too low.
verbose logical, whether to print out info.
usePeaks logical, TRUE uses peakdata list, FALSE uses rawdata list for computing similarity.
compress logical, whether to compress the similarity matrix into a sparse format.

Details

peaksAlignment is a hold-all data structure of the raw and peak detection data.

Value

peaksAlignment object

Author(s)

Mark Robinson

References

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

See Also

peaksDataset, clusterAlignment

Examples


# see clusterAlignment, it calls peaksAlignment


[Package flagme version 1.0.0 Index]