EvaluateCandidateListAgainstRawData: EvaluateCandidateListAgainstRawData.

In HiResTEC: Non-Targeted Fluxomics on High-Resolution Mass-Spectrometry Data

EvaluateCandidateListAgainstRawData.

Description

EvaluateCandidateListAgainstRawData will analyze an xcmsSet result for mass pairs (mz1, mz2) with changes due to 13C incorporation.

Usage

EvaluateCandidateListAgainstRawData(
  x = NULL,
  tp = NULL,
  gr = NULL,
  dat = NULL,
  dmz = 0.025,
  drt = 1,
  dEcut = 1,
  Pcut = 0.01,
  Icut = 1000,
  method = c("APCI", "ESI")[1],
  rolp = c("non", "pos", "neg", "all")[2],
  smooth = 0
)

Arguments

x	Dataframe of results (output of EvaluatePairsFromXCMSet).
tp	Timepoint.
gr	group, e.g. different genotypes or concentrations.
dat	list of xcmsRaw's for deconvolution and plotting.
dmz	Allowed mass deviation in Da (for BPC extraction).
drt	Allowed rt deviation in seconds (for get extraction).
dEcut	Minimum required change in enrichment before a candidate ID is assigned.
Pcut	Maximum allowed P value before a candidate ID is assigned.
Icut	Minimum required median peak intensity before a candidate ID is assigned.
method	Either APCI or ESI. Choice will modify some internal parameters and checks performed.
rolp	RemoveOverLappingPeaks paramter.
smooth	Smoothing parameter passed to getMultipleBPC.

Details

This function will evaluate candidate mz pairs found within an xcmsSet object by EvaluatePairsFromXCMSSet against the raw measurement data. A special parameter is 'rolp' which can be set to 'non', 'pos', 'neg' or 'all'. It will influence the time performance of the function be determining how many peaks are effectively tested. If 'rolp' is set to 'non', no overlapping peaks will be skipped, every individual mz-pair will be sequentially evaluated (slow but most informative). If it is set to 'pos' or 'neg', overlapping peaks (determined by experiment wide deconvolution) will not be tested aditionally for positive or negative hits ('neg' is standard). If set to 'all' overlapping peaks will always be removed from the list of mz-pairs to be tested (fast).

Value

A list of evaluation results.

Examples

# Please use examples from previous versions as xcms (and xcms objects)
# are no longer supported during CRAN checks leading to package rejection
# if included (and I do not know a work around). :(

HiResTEC documentation built on March 7, 2023, 5:47 p.m.