PuInc_seeker: Detect Putative Incorporation features
In jcapelladesto/geoRge: Isotopic label tracking for untargeted metabolomics

Description Usage Arguments Value Examples

Use Welch's T-test to detect features upregulated in labelled samples

PuInc_seeker(
  XCMSet = NULL,
  XCMSmode = "maxo",
  ULtag = NULL,
  Ltag = NULL,
  separator = "_",
  sep.pos.front = TRUE,
  fc.threshold = 1.2,
  p.value.threshold = 0.05,
  PuInc.int.lim = NULL
)

`XCMSet`	xcmsSet or XCMSnExp object of samples processed by xcms workflow
`XCMSmode`	Type of quantification value for the features, as in `xcms::groupval(XCMSet)`
`ULtag`	Unlabelled sample name tag, for example "C12"
`Ltag`	Labelled sample name tag, for example "C13"
`separator`	Character used as separator in sample names, as in `xcms::sampclass(XCMSet)`
`sep.pos.front`	`TRUE` if position of `ULtag` and `Ltag` is found previous to the condition names. Check `xcms::sampclass(XCMSet)`
`fc.threshold`	Fold-change threshold for detection of upregulated features associated to Putative incorporation
`p.value.threshold`	p-Value threshhold between for detection of upregulated features associated to Putative incorporation
`PuInc.int.lim`	Intensity limit in UNlabelled sample for the selection of features to be tested as possible Putative incorporation

A list containing:

PuInc: Putative Incorporation Features matrix
PuInc_conditions: Experimetal conditions (as in xcms::sampclass(XCMSet)) in which PuInc were detected
pvalue: Matrix of p-values from the tested features
foldchange: Matrix of fold-changes from the tested features
params: Inputed arguments to be inherited by basepeak_finder

data(mtbls213)
xcms::sampclass(mtbls213)
PuInc_seeker(XCMSet=mtbls213,ULtag="CELL_Glc12",Ltag="CELL_Glc13",
sep.pos.front=TRUE ,fc.threshold=1.5,p.value.threshold=.05,PuInc.int.lim = 4000)