prioritizer: Prioritize Samples
In chasemc/IDBacApp: MALDI-TOF MS Protien and Small Molecule Analysis

prioritizer

R Documentation

Prioritize Samples

Description

Prioritize Samples

Usage

prioritizer(
  pool,
  dendrogram,
  h = NULL,
  k = NULL,
  fractionMetabolitePeaksToRetain,
  minFrequency = 0,
  minNumber = NA,
  smallMolLowerMassCutoff = 200,
  smallMolUpperMassCutoff = 2000,
  smallMolSnr = 10,
  tolerance = 0.002,
  method = "strict"
)

Arguments

`pool`	pool connection to IDBac database
`dendrogram`	dendrogram object to be cut, doesn't necessarily have to be protein dendrogram but labels should be the same as the small molecule data labels
`h`	numeric scalar (OR a vector) with a height where the tree should be cut.
`k`	numeric scalar (OR a vector) with the number of clusters the tree should be cut into.
`fractionMetabolitePeaksToRetain`	fraction of small molecule peaks to "capture" when selecting isolates
`minFrequency`	percent of peaks that must be present in sample replicates (0 to 1)
`minNumber`	`double`, remove all peaks which occur in less than `minNumber` `MassPeaks` objects. It is an absolute threshold.
`smallMolLowerMassCutoff`	lower mass cutoff for small molecule spectra
`smallMolUpperMassCutoff`	upper mass cutoff for small molecule spectra
`smallMolSnr`	minimum SNR for small molecule spectra
`tolerance`	`double`, maximal relative deviation of a peak position (mass) to be considered as identical. Must be multiplied by `10^-6` for ppm, e.g. use `tolerance=5e-6` for 5 ppm.
`method`	bin creation rule. `"strict"` creates bins never containing two or more peaks of the sampe sample. `"relaxed"` allows multiple peaks of the same sample in one bin.