Description Usage Arguments Value References See Also
View source: R/do_groupChromPeaks-functions.R
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).
1 2 3 4 5 6 7 8 | 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:
"mzmed"
: median of the peaks' apex mz values.
"mzmin"
: smallest mz value of all peaks' apex within the feature.
"mzmax"
:largest mz value of all peaks' apex within the feature.
"rtmed"
: the median of the peaks' retention times.
"rtmin"
: the smallest retention time of the peaks in the feature.
"rtmax"
: the largest retention time of the peaks in the feature.
"npeaks"
: 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()
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