idbac_get_peaks: Collapse a sample's MALDIquant peak objects into a single...
In chasemc/IDBacApp: MALDI-TOF MS Protien and Small Molecule Analysis

idbac_get_peaks

R Documentation

Collapse a sample's MALDIquant peak objects into a single peak object

Description

Collapse a sample's MALDIquant peak objects into a single peak object

Usage

idbac_get_peaks(
  pool,
  sampleIDs,
  minFrequency = 0,
  minNumber = NA,
  lowerMassCutoff,
  upperMassCutoff,
  minSNR,
  tolerance = 0.002,
  type,
  mergeReplicates = TRUE,
  method = "strict",
  verbose = FALSE
)

Arguments

`pool`	sqlite pool
`sampleIDs`	sample IDs of samples to process
`minFrequency`	`double`, remove all peaks which occur in less than `minFrequency*length(l)` `MassPeaks` objects. It is a relative threshold.
`minNumber`	`double`, remove all peaks which occur in less than `minNumber` `MassPeaks` objects. It is an absolute threshold.
`lowerMassCutoff`	masses below this will be removed from analyses
`upperMassCutoff`	masses above this will be removed from analyses
`minSNR`	minimum SNR a a peak must have to be retained
`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.
`type`	"protein", "small", or "all"
`mergeReplicates`	should replicates be merged? TRUE/FALSE
`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.
`verbose`	should minfreq/minnum warning be displayed