groupFeaturesOpenMS: Group features using OpenMS

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

Group features using OpenMS

Description

Group and align features with OpenMS tools

Usage

groupFeaturesOpenMS(feat, ...)

## S4 method for signature 'features'
groupFeaturesOpenMS(
  feat,
  rtalign = TRUE,
  QT = FALSE,
  maxAlignRT = 30,
  maxAlignMZ = 0.005,
  maxGroupRT = 12,
  maxGroupMZ = 0.005,
  extraOptsRT = NULL,
  extraOptsGroup = NULL,
  verbose = TRUE
)

Arguments

feat	The features object with the features to be grouped.
...	Further parameters passed to the selected grouping algorithm.
rtalign	Set to TRUE to enable retention time alignment.
QT	If enabled, use FeatureLinkerUnlabeledQT instead of FeatureLinkerUnlabeled for feature grouping.
maxAlignRT, maxAlignMZ	Used for retention alignment. Maximum retention time or m/z difference (seconds/Dalton) for feature pairing. Sets -algorithm:pairfinder:distance_RT:max_difference and -algorithm:pairfinder:distance_MZ:max_difference otpions, respectively.
maxGroupRT, maxGroupMZ	as maxAlignRT and maxAlignMZ, but for grouping of features. Sets -algorithm:distance_RT:max_difference and -algorithm:distance_MZ:max_difference options, respectively.
extraOptsRT, extraOptsGroup	Named list containing extra options that will be passed to MapAlignerPoseClustering or FeatureLinkerUnlabeledQT/FeatureLinkerUnlabeled, respectively. Any options specified here will override any of the above. Example: extraOptsGroup=list("-algorithm:distance_RT:max_difference"=12) (corresponds to setting maxGroupRT=12). Set to NULL to ignore.
verbose	if FALSE then no text output will be shown.

Details

This function uses OpenMS to group features. This function is called when calling groupFeatures with algorithm="openms".

Retention times may be aligned by the MapAlignerPoseClustering TOPP tool. Grouping is achieved by either the FeatureLinkerUnlabeled or FeatureLinkerUnlabeledQT TOPP tools.

Value

An object of a class which is derived from featureGroups.

The featuresSet method (for sets workflows) returns a featureGroupsSet object.

References

\insertRef

Rst2016patRoon

pugixml (via Rcpp) is used to process OpenMS XML output.

\addCitationsRcpp1

\addCitationsRcpp2

\addCitationsRcpp3

See Also

groupFeatures for more details and other algorithms.

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