findFeaturesKPIC2: Find features using KPIC2

In rickhelmus/patRoon: Workflows for Mass-Spectrometry Based Non-Target Analysis

Find features using KPIC2

Description

Uses the KPIC2 R package to extract features.

Usage

findFeaturesKPIC2(
  analysisInfo,
  kmeans = TRUE,
  level = 1000,
  ...,
  parallel = TRUE,
  verbose = TRUE
)

Arguments

analysisInfo	A data.frame with Analysis information.
kmeans	If TRUE then getPIC.kmeans is used to obtain PICs, otherwise it is getPIC.
level	Passed to getPIC or getPIC.kmeans
...	Further parameters passed to getPIC/getPIC.kmeans
parallel	If set to TRUE then code is executed in parallel through the futures package. Please see the parallelization section in the handbook for more details.
verbose	If set to FALSE then no text output is shown.

Details

This function uses KPIC2 to automatically find features. This function is called when calling findFeatures with algorithm="kpic2".

The MS files should be in the mzML or mzXML format.

The input MS data files need to be centroided. The convertMSFiles function can be used to centroid data.

Value

An object of a class which is derived from features.

References

\insertRef

Ji2017patRoon

See Also

findFeatures for more details and other algorithms.

rickhelmus/patRoon documentation built on Nov. 22, 2024, 3:11 p.m.