ApexIntensityOptions (BioFSharp)

ApexIntensityOptions Type

Namespace: BioFSharp.BioContainers
Assembly: BioFSharp.BioContainers.dll
Parent Module: MoFF
Base Type: obj
All Interfaces: IEquatable<ApexIntensityOptions> , IStructuralEquatable , IComparable<ApexIntensityOptions> , IComparable , IStructuralComparable

Those options run the Apex Intensity module. Around the RT of the input feature, a time window is constructed which results in a local XIC. The peak apex is then located in this local XIC. The log_L_R metric measures the skewness of the peak around the RT of the obtained apex point. The SNR metric provides the ratio of peak height to noise, where the noise value is set as the lowest intensity value in the local XIC. mzML must be specified using --tsv_list | --raw_list (Ms2PeptidesInputFile & RawFile)

Union cases

Union case	Description
`FilterMatchedPeak bool` Full Usage: `FilterMatchedPeak bool` Parameters: Item : `bool`	--match_filter If set, filtering on the matched peak is activated. Default value: False Item : `bool`
`FilteringThresholdQuantileValue float` Full Usage: `FilteringThresholdQuantileValue float` Parameters: Item : `float`	--quantile_thr_filtering quantile value used to computed the filtering threshold for the matched peak . Default is 0.75 Item : `float`
`GetPeakInRtWindow float` Full Usage: `GetPeakInRtWindow float` Parameters: Item : `float`	--rt_peak_win time windows used to get the apex for the ms2 peptide/feature (minutes). Default value is 1 Item : `float`
`GetPeakInRtWindowForMatches float` Full Usage: `GetPeakInRtWindowForMatches float` Parameters: Item : `float`	--rt_peak_win_match time windows used to get the apex for machted features (minutes). Default value is 1.2 Item : `float`
`MassTolerance int` Full Usage: `MassTolerance int` Parameters: Item : `int`	--tol mass tollerance (ppm) Item : `int`
`OutputFileFolder string` Full Usage: `OutputFileFolder string` Parameters: Item : `string`	--loc_out output folder Item : `string`
`PeptideSummaryFile` Full Usage: `PeptideSummaryFile`	--peptide_summary flag that allows have as output the peptided summary intensity file. Default is disable(0)
`PeptideSummaryFileName string` Full Usage: `PeptideSummaryFileName string` Parameters: Item : `string`	--tag_pepsum a tag that is used in the peptide summary file name Item : `string`
`PtmFile string` Full Usage: `PtmFile string` Parameters: Item : `string`	--ptm_file modification json ptm file. Default file ptm_setting.json Item : `string`
`RtWindow float` Full Usage: `RtWindow float` Parameters: Item : `float`	--xic_length rt windows for xic (minutes). Default value is 3 min Item : `float`
`SampleSizeForThreshold float` Full Usage: `SampleSizeForThreshold float` Parameters: Item : `float`	--sample_size percentage of MS2 identified peptides used to estimated the threshold Item : `float`

Static members

Static member Description

Static member	Description
`ApexIntensityOptions.make` Full Usage: `ApexIntensityOptions.make` Returns: `ApexIntensityOptions -> string list`	Returns: `ApexIntensityOptions -> string list`
`ApexIntensityOptions.makeWith m` Full Usage: `ApexIntensityOptions.makeWith m` Parameters: m : `MountInfo` Returns: `ApexIntensityOptions -> string list`	m : `MountInfo` Returns: `ApexIntensityOptions -> string list`


                
                  
                    
                      ApexIntensityOptions.make

Full Usage: ApexIntensityOptions.make

Returns: ApexIntensityOptions -> string list

Returns: ApexIntensityOptions -> string list


                
                  
                    
                      ApexIntensityOptions.makeWith m

Full Usage: ApexIntensityOptions.makeWith m

Parameters:

m : MountInfo

Returns: ApexIntensityOptions -> string list

m : MountInfo

Returns: ApexIntensityOptions -> string list