dmzgap given in ppm (TRUE) or as absolute value (FALSE)?
drtgap
RT gap width for partitioning
minpeak
Minimum number of measurements in a partition
maxint
Measurements equal or above this intensity will be retained even if ranging below minpeak
progbar
For debugging, ignore
Details
Partitioning of the full set of measurements into subsets is necessary to speed up the clustering procedure of mzclust.
To this end, an agglomerative partitioning approach is used, combining measurements that are linked by values smaller than drtgap and
dmzgap into single subsets. No measurements of two different subsets can be closer than drtgap and dmzgap to each other.
Value
Returns the argument MSlist, with entries made:
Parameters
MSlist[[2]]: saves the parameter settings.
Scans
MSlist[[4]]: matrix with raw measurements and tags resorted for partitions.
Partition_Index
MSlist[[5]]: Index assigning partitions to sections in the raw measurement of MSlist[[4]]; required for fast (random) access.
Imbecile
Do not set minpeak bigger than its counterpart in mzclust or mzpick.
Too complicated? Then rather use enviPickwrap for adjusting all function arguments.
Warning
Despite optimized code, this function has a potential to run for a intolerable long time or out of memory if (a) the parameters are set wrongly, (b) the .mzML/.mzXML-file was not centroided or
(c) the underlying data is inadequate for this peak picker.
With regards to (a), do not assume gaps being larger than actually present. Instead, use plotMSlist to have a look at your
data contained in MSlist after upload with readMSdata.