flagme (version 1.28.0)

peaksAlignment-class: 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.

Value

peaksAlignment object

Details

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

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