do_groupChromPeaks_nearest {xcms} | R Documentation |
The do_groupChromPeaks_nearest
function groups peaks
across samples by creating a master peak list and assigning corresponding
peaks from all samples to each peak group (i.e. feature). The method is
inspired by the correspondence algorithm of mzMine [Katajamaa 2006].
do_groupChromPeaks_nearest(peaks, sampleGroups, mzVsRtBalance = 10, absMz = 0.2, absRt = 15, kNN = 10)
peaks |
A |
sampleGroups |
A vector of the same length than samples defining the
sample group assignments (i.e. which samples belong to which sample
group). This parameter is mandatory for the |
mzVsRtBalance |
|
absMz |
|
absRt |
|
kNN |
|
A list
with elements "featureDefinitions"
and
"peakIndex"
. "featureDefinitions"
is a matrix
, each row
representing an (mz-rt) feature (i.e. peak group) with columns:
median of the peaks' apex mz values.
smallest mz value of all peaks' apex within the feature.
largest mz value of all peaks' apex within the feature.
the median of the peaks' retention times.
the smallest retention time of the peaks in the feature.
the largest retention time of the peaks in the feature.
the total number of peaks assigned to the feature.
"peakIndex"
is a list
with the indices of all peaks in a
feature in the peaks
input matrix.
Katajamaa M, Miettinen J, Oresic M: MZmine: Toolbox for processing and visualization of mass spectrometry based molecular profile data. Bioinformatics 2006, 22:634-636.
Other core peak grouping algorithms: do_groupChromPeaks_density
,
do_groupPeaks_mzClust