fillPeaks.chrom-methods: Integrate areas of missing peaks

Description Arguments Details Value Methods See Also


For each sample, identify peak groups where that sample is not represented. For each of those peak groups, integrate the signal in the region of that peak group and create a new peak.



the xcmsSet object


number of slaves/cores to be used for parallel peak filling. MPI is used if installed, otherwise the snow package is employed for multicore support.


After peak grouping, there will always be peak groups that do not include peaks from every sample. This method produces intensity values for those missing samples by integrating raw data in peak group region. In a given group, the start and ending retention time points for integration are defined by the median start and end points of the other detected peaks. The start and end m/z values are similarly determined. Intensities can be still be zero, which is a rather unusual intensity for a peak. This is the case if e.g. the raw data was threshholded, and the integration area contains no actual raw intensities, or if one sample is miscalibrated, such thet the raw data points are (just) outside the integration area.

Importantly, if retention time correction data is available, the alignment information is used to more precisely integrate the propper region of the raw data. If the corrected retention time is beyond the end of the raw data, the value will be not-a-number (NaN).


A xcmsSet objects with filled in peak groups (into and maxo).


object = "xcmsSet"

fillPeaks.chrom(object, nSlaves=0)

See Also

xcmsSet-class, getPeaks fillPeaks

sneumann/xcms-presvnbridge documentation built on May 30, 2019, 6:02 a.m.