mzDeco


        require(mzkit);
                               

#' Extract peak and signal data from rawdata
imports "mzDeco" from "mz_quantify";

Extract peak and signal data from rawdata Data processing is the computational process of converting raw LC-MS data to biological knowledge and involves multiple processes including raw data deconvolution and the chemical identification of metabolites. The process of data deconvolution, sometimes called peak picking, is in itself a complex process caused by the complexity of the data and variation introduced during the process of data acquisition related to mass-to-charge ratio, retention time and chromatographic peak area.

.NET clr type export
peak_feature: PeakFeature	a result peak feature
mz_group: MzGroup	XIC dataset that used for deconv
peak_set: PeakSet	A collection of the xcms2 peak features data
xcms2: xcms2	the peak table format table file model of xcms version 2
rt_shift: RtShift	the rt shift result
RI_refer: RIRefer	the retention index reference

.NET clr function exports
as.data.frame.peakset	PeakSet: A collection of the xcms2 peak features data
as.data.frame.xcms2	xcms2: the peak table format table file model of xcms version 2
as.data.frame.peakfeature	PeakFeature: a result peak feature
readBin.stream	Stream:
readBin.stream	Stream:
readBin.stream	Stream:
writeBin.peakset	PeakSet: A collection of the xcms2 peak features data
writeBin.peakfeature	PeakFeature: a result peak feature
writeBin.mzgroup	MzGroup: XIC dataset that used for deconv
writeBin.mzgroup	MzGroup: XIC dataset that used for deconv
read.xcms_peaks	read the peaktable file that in xcms2 output format
to_expression	cast peaktable to expression matrix object
to_matrix	cast peaktable to mzkit expression matrix
write.xcms_peaks	save mzkit peaktable object to csv table file
as.peak_set	cast dataset to mzkit peaktable object
read.xcms_features	Try to cast the dataframe to the mzkit peak feature object set
peak_subset	make sample column projection
xcms_peak	Create a xcms peak data object
find_xcms_ionPeaks	helper function for find ms1 peaks based on the given mz/rt tuple data
get_xcms_ionPeaks	get ion peaks via the unique reference id
adjust_to_seconds	adjust the reteintion time data to unit seconds
RI_reference	Create RI reference dataset.
RI_cal	RI calculation of a speicifc sample data
mz_deco	Chromatogram data deconvolution
MS1deconv	A debug function for test peak finding method
read.rt_shifts
write.peaks	write peak debug data
read.peakFeatures	read the peak feature table data
peak_alignment	Do COW peak alignment and export peaktable Correlation optimized warping (COW) based on the total ion current (TIC) is a widely used time alignment algorithm (COW-TIC). This approach works successfully on chromatograms containing few compounds and having a well-defined TIC.
RI_batch_join	make peaktable join of two batch data via (mz,RI)
mz.groups	do `m/z` grouping under the given tolerance
xic_pool	Load xic sample data files
pull_xic	extract a collection of xic data for a specific ion feature this function is debug used only