resetFIR-peakPantheRAnnotation-method: Reset FIR windows to uROI or ROI values Reset FIR windows to...

In phenomecentre/peakPantheR: Peak Picking and Annotation of High Resolution Experiments

Reset FIR windows to uROI or ROI values Reset FIR windows to uROI (or ROI if uROIExist=FALSE)

Description

Reset FIR windows to uROI or ROI values Reset FIR windows to uROI (or ROI if uROIExist=FALSE)

Usage

## S4 method for signature 'peakPantheRAnnotation'
resetFIR(object, verbose)

Arguments

object	(peakPantheRAnnotation) object for which FIR are to be reset
verbose	(bool) If TRUE message progress

Value

(peakPantheRAnnotation) object with FIR values reset

Examples

## Initialise a peakPantheRAnnotation object with 2 targeted compounds

## targetFeatTable
input_targetFeatTable <- data.frame(matrix(vector(), 2, 8,
                            dimnames=list(c(), c('cpdID', 'cpdName', 'rtMin',
                            'rt', 'rtMax', 'mzMin', 'mz', 'mzMax'))),
                            stringsAsFactors=FALSE)
input_targetFeatTable[1,] <- c('ID-1', 'Cpd 1',  3.,  1.,  4.,  5.,  2.,  6.)
input_targetFeatTable[2,] <- c('ID-2', 'Cpd 2', 19., 17., 20., 21., 18., 22.)
input_targetFeatTable[,c(3:8)] <- sapply(input_targetFeatTable[,c(3:8)],
                                        as.numeric)
## FIR
input_FIR       <- data.frame(matrix(vector(), 2, 4, dimnames=list(c(), 
                                c('rtMin', 'rtMax', 'mzMin', 'mzMax'))),
                                stringsAsFactors=FALSE)
input_FIR[1,]   <- c(13., 14., 15., 16.)
input_FIR[2,]   <- c(29., 30., 31., 32.)

annotation <- peakPantheRAnnotation(targetFeatTable = input_targetFeatTable,
                                    FIR = input_FIR, uROIExist = FALSE)

## Reset FIR with ROI values as uROI are not set
updatedAnnotation <- resetFIR(annotation, verbose=TRUE)
# FIR will be reset with ROI values as uROI values are not set

phenomecentre/peakPantheR documentation built on Feb. 29, 2024, 9:07 p.m.