ExtractParam: Isotopoluage extraction parameter setup
In ZhuMetLab/MetTracer: Tracing isotope labelled metabolites

View source: R/methods-Params.R

ExtractParam

R Documentation

Isotopoluage extraction parameter setup

Description

Isotopoluage extraction parameter setup

Usage

ExtractParam(
  d.extract = "extract",
  range.extract = c("all", "roi", "rtrange"),
  method.align = c("apex", "eic"),
  method.best = c("maxint", "maxcor"),
  method.quant = c("rawinroi", "raw", "baseline"),
  nscan.quant = 3,
  minfrac = 0.5,
  adj.unlabel = NULL,
  adj.label = NULL,
  adj.contaminate = FALSE,
  thr.contaminate = 0.02
)

Arguments

`d.extract`	directory of samples to be extracted
`range.extract`	EIC extraction range [] 'all' - extract the entire eic [] 'roi' - extract the rois related to rt range of target peaks []'rtrange' - extract the eic at the range of rt range of target peaks
`method.align`	method for creating representative peak profile [] 'apex' align with the apex of the most similar peaks [] 'eic' align with the correlation of the eics from unlabelled and labelled samples
`method.best`	method for finding best correlated peak groups for extracted isotopoluage to determine the rt range of extracted peaks/eics [] 'maxint' select the highest peak as rt range reference [] 'maxcor select the most similar peak to representive peak as rt range reference @param method.quant method for quantifying extracted isotopic peaks. [] 'rawinroi' sum with raw intensities of significant scans (in ROI) [] 'baseline' baseline substraxted rawinroi method [] 'raw' sum with raw intensities anyway
`nscan.quant`	number of scans to sum up for quantifying
`minfrac`	minimal fraction threshold to determine the isotopic peak existed or not in the sample groups
`adj.unlabel`	character vector, group names of unlabelled samples for adjusting the isotopoluage of labelled samples
`adj.label`	character vector, group names of labelled samples to be adjusted using the unlabelled samples (pairwised with the sample groups in `adj.unlabel`)
`adj.contaminate`	logical: if adjust the contaminate using unlabelled samples, if `TRUE`, `adj.unlabel` and `adj.label` must be set