mergeRCobjects: mergeRCobjects

In cbroeckl/RAMClustR: Mass Spectrometry Metabolomics Feature Clustering and Interpretation

mergeRCobjects

Description

merge two ramclustR objects

Usage

mergeRCobjects(
  ramclustObj.1 = NULL,
  ramclustObj.2 = NULL,
  mztol = 0.02,
  rttol = 30,
  course.rt.adj = NULL,
  mzwt = 2,
  rtwt = 1,
  intwt = 3
)

Arguments

ramclustObj.1	ramclustR object 1: this object will be the base for the new object. That is all the features from ramclustObj.1 will be retained.
ramclustObj.2	ramclustR object 2: this object will mapped and appended to racmlustObj1. That is only features which appear consistent with those from ramclustObj.1 will be retained.
mztol	numeric: absolute mass tolerance around mz
rttol	numeric: feature retention time tolerance. Value set by this option will be used during the initial anchor mapping phase. Two times the standard error of the rt loess correction will be used for the full mapping.
course.rt.adj	numeric: default = NULL. optional approximate retention time shift between ramclustObj.1 and ramclustObj.2. i.e if the retention time of ramclustObj.1 is on average 15 seconds longer than that of ramclustobj.2, enter '15'. if 1 is less than 2, enter a negative number. This is applied before mapping to enable a smaller 'rttol' value to be used.
mzwt	numeric: when mapping features, weighting value used for similarities between feature mass values (see rtwt, intwt)
rtwt	numeric: when mapping features, weighting value used for similarities between feature retention time values (see mzwt, intwt)
intwt	numeric: when mapping features, weighting value used for similarities between ranked signal intensity values (see rtwt, mzwt)

Details

Two ramclustR objects are merged with this function, mapping features between them. The first (ramclustObj.1) object use used as the template - all data in it is retained. ramclustObj.2 is mapped to ramclustObj.1 feature by feature - only mapped features are retained. A new ramlcustObj is returned, with a new SpecAbund dataset with the same column number as the ramclustObj.1$SpecAbund set.

Value

returns a ramclustR object. All values from ramclustObj.1 are retained. SpecAbund dataset from ramclustObj.1 is moved to RC$SpecAbund.1, where RC is the new ramclustObj.

Author(s)

Corey Broeckling

cbroeckl/RAMClustR documentation built on Sept. 1, 2024, 1:50 a.m.