MassSpecSettings_LoadMSPeakLists_StreamFind
Source:R/class_S3_MassSpecSettings.R
MassSpecSettings_LoadMSPeakLists_StreamFind.RdSettings for converting loaded MS2 and MS1 spectra into a MSPeakLists object from patRoon.
Usage
MassSpecSettings_LoadMSPeakLists_StreamFind(
clusterMzWindow = 0.005,
topMost = 100,
minIntensityPre = 50,
minIntensityPost = 50,
avgFun = mean,
method = "distance"
)Arguments
- clusterMzWindow
m/z window (in Da) used for clustering m/z values when spectra are averaged. For method="hclust" this corresponds to the cluster height, while for method="distance" this value is used to find nearby masses (+/- window). Too small windows will prevent clustering m/z values (thus erroneously treating equal masses along spectra as different), whereas too big windows may cluster unrelated m/z values from different or even the same spectrum together.
- topMost
Only retain this maximum number of MS peaks when generating averaged spectra. Lowering this number may exclude more irrelevant (noisy) MS peaks and decrease processing time, whereas higher values may avoid excluding lower intense MS peaks that may still be of interest.
- minIntensityPre
MS peaks with intensities below this value will be removed (applied prior to selection by
topMost) before averaging.- minIntensityPost
MS peaks with intensities below this value will be removed after averaging.
- avgFun
Function that is used to calculate average m/z values.
- method
Method used for producing averaged MS spectra. Valid values are "hclust", used for hierarchical clustering (using the fastcluster package), and "distance", to use the between peak distance. The latter method may reduces processing time and memory requirements, at the potential cost of reduced accuracy.