peaksAlignment-class {flagme} | R Documentation |
Store the raw data and optionally, information regarding signal peaks for a number of GCMS runs
peaksAlignment(d1,d2,t1,t2,gap=.5,D=1000,timedf=NULL,df=30,verbose=TRUE,usePeaks=TRUE,compress=TRUE)
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. |
peaksAlignment is a hold-all data structure of the raw and peak detection data.
peaksAlignment
object
Mark Robinson
Mark D Robinson (2008). Methods for the analysis of gas chromatography - mass spectrometry data PhD dissertation University of Melbourne.
peaksDataset
, clusterAlignment
# see clusterAlignment, it calls peaksAlignment