Function reference • cpc

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`calculatePeakCharacteristics(<cpc_chrom>)`	Internal method for calculation of the peak characteristics
`characterize_xcms_peaklist()`	Wrapper function for characterization of the peaks detected by XCMS
`checkPeaksAgainstCriteria(<cpc>)`	Method that check each peak in the XCMS object against the criteria specified by the user in the cpcProcParam object
`chromFromTrace()`	Create a cpc_chrom object from a chromatogram trace
`cpc-class`	cpc class
`getPeaklist(<cpc>)` `cpt(<cpc>)` `getProcData(<cpc>)` `setProcData<-`(<cpc>) `setProcData<-`(<cpc>) `getProcParams(<cpc>)` `getParam(<cpc>)` `setParam<-`(<cpc>) `parsePeaklist(<cpc>)` `getChromatogram(<cpc>)` `processPeaks(<cpc>)` `getFilterOutcomes(<cpc>)` `filterPeaks(<cpc>)` `getOriginalXCMS(<cpc>)` `getFilteredXCMS(<cpc>)` `getRemovedPeaks(<cpc>)` `getRetainedPeaks(<cpc>)` `show(<cpc>)`	Getter method for the parsed peak table in a `cpc` object
`cpc-package`	Comprehensive Peak Characterization of LC/GC-MS Data
`cpcChromParam-class`	Class cpcChromParam
`cpcChromParam()`	Constructor for a cpcChromParam object
`setParam<-`(<cpcParam>) `getParam(<cpcParam>)`	Setter method for the parameter slot
`cpcProcParam-class`	Class cpcProcParam
`cpcProcParam()`	Constructor for a cpcProcParam object
`cpc_chrom-class`	Class used to process an XIC and calculate peak characteristics
`getProcData(<cpc_chrom>)` `setProcData<-`(<cpc_chrom>) `plotPeak(<cpc_chrom>)` `processChromatogram(<cpc_chrom>)`	Getter method for the procData slot
`cpc_raw-class`	Class for handling the MS raw data backend
`cpt<-`(<cpc>)	Setter method for the `cpt` slot in a `cpc` object
`fast_match()`	Matches a vector of integers in a second vector of integers
`filePaths(<cpc>)`	Getter for the `procData$file_paths` slot in a `cpc` object
`filter_xcms_peaklist()`	Wrapper function for filter the peaks detected by XCMS
`filteredObject(<cpc>)`	Getter method that returns the filtered `XCMSnExp` object.
`getMzRange(<cpc_chrom>)`	Getter for mz range parameter
`getProcParams(<cpc_chrom>)`	Getter method for the procParams slot
`getResults(<cpc_chrom>)`	Getter method for the results slot
`getXIC(<cpc_raw>)`	Method to generate an XIC from a `cpc_raw` object
`hasCharacterizedPeakTable(<cpc>)`	Method to check if a `cpc` object has a characterized peaktable
`hasPeakTable(<cpc>)`	Method to check if a `cpc` object has a parsed peaktable
`parseMz(<cpc_raw>)`	Parsing method for the MS raw data contained in the specified file
`peaksToKeep(<cpc>)`	Method to generate an idx vector of peaks that pass the filter criteria after peak characterization.
`plotPeaks()`	Plotting of characterized peaks
`process_chromatogram()`	Rcpp wrapper that calls the C++ chromatogram processing framework
`scantime(<cpc_raw>)`	Getter method for the scantime vector in a `cpc_raw` object
`setPeaklist<-`(<cpc>)	Setter method for the parsed peak table in a `cpc` object
`setProcParams<-`(<cpc>)	Setter method for the procParams slot
`setProcParams<-`(<cpc_chrom>)	Setter method for the procParams slot
`setResults<-`(<cpc_chrom>)	Setter method for the results slot
`setXIC<-`(<cpc_chrom>)	Setter method for the XIC slot
`show(<cpcParam>)`	Show method for the cpcParam object
`smoothChromatogram(<cpc_chrom>)`	Method for calculating smoothed XICs in a cpc_chrom object.
`xdObj(<cpc>)`	Getter method for the `XCMSnExp` object contained in a `cpc` object
`xdObj<-`(<cpc>)	Setter method for the `XCMSnExp` object slot in a `cpc` object

Reference

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