rtDevModelling {adductomicsR} | R Documentation

## MS/MS spectrum grouping and retention time deviation modelling for adductomicsR

### Description

MS/MS spectrum grouping and retention time deviation modelling for adductomicsR

### Usage

    rtDevModelling(MS2Dir = NULL, runOrder = NULL,
    nCores = NULL, TICfilter = 0,
    intStdPeakList=c(290.21, 403.30, 516.38, 587.42,849.40, 884.92, 958.46,
    993.97,1050.52, 1107.06, 1209.73, 1337.79,1465.85),
    intStdMass = 834.77692, intStd_MaxMedRtDrift = 600, intStd_MaxPpmDev = 200,
    minSpecEx = 40,
    minDotProd = 0.8, percMissing = 15, percExtra = 100, smoothingSpan = 0.8,
    saveRtDev = 1, outputPlotDir = NULL)

### Arguments

`MS2Dir` | character a full path to a directory containing either .mzXML or .mzML data
`runOrder` | character a full path to a csv file specifying the runorder for each of the files the first column must contain the precise file name and the second column an integer representing the precise run order.
`nCores` | numeric the number of cores to use for parallel computation. The default is to 1 core.
`TICfilter` | numeric minimimum total ion current of an MS/MS scan. Any MS/MS scan below this value will be filtered out (default=0).
`intStdPeakList` | character a comma seperated list of expected fragment ions for the internal standard spectrum (no white space).
`intStdMass` | numeric expected mass-to-charge ratio of internal standard precursor (default = 834.77692).
`intStd_MaxMedRtDrift` | numeric the maximum retention time drift window (in seconds) to identify internal standard MS/MS spectrum scans (default = 600).
`intStd_MaxPpmDev` | numeric the maximum mass accuracy window (in ppm) to identify internal standard MS/MS spectrum scans (default = 200 ppm).
`minSpecEx` | numeric the minimum percentage of the total ion current explained by the internal standard fragments (default = 40). Sometimes spectra are not identified due to this cutoff being set too high. If unexpected datapoints have been interpolated then reduce this value.
`minDotProd` | numeric. Minimum mean dot product spectral similarity score to keep a spectrum within an MS/MS group (default = 0.8).
`percMissing` | numeric. percentage of missing files for a MS/MS scan group to be utilized in the loess retention time deviation model. Roughly 15 percent missing values (default = 15%) is a good starting point (e.g. nMissing=10 for 68 samples).
`percExtra` | numeric percentage of extra scans above the total number of files for a MS/MS scan group to be utilized in the loess retention time deviation model. If a MS/MS scan group consists of many scans far in excess of the number of files then potentially MS/MS scans from large tailing peaks or isobars may be erroneously grouped together and used to adjust retention time incorrectly (default = 100% i.e. the peak group can only have one scan per file, this value can be increased if two or more consecutive scans for example can be considered).
`smoothingSpan` | numeric. fixed smoothing span, argument to `loess`. If argument is not supplied then optimal smoothing span is calculated for each file seperately using 7-fold CV.
`saveRtDev` | integer (default = 1) should just the retention time deviation model be saved (TRUE = 1) or the AdductSpec class object (FALSE = 0) as .RData workspace files.
`outputPlotDir` | character (default = NULL) output directory for plots.

### Value

LOESS RT models as adductSpectra AdductSpec object

### Examples

    eh = ExperimentHub();
    temp = query(eh, 'adductData');
    temp[['EH2061']]; #first mzXML file
    file.rename(cache(temp["EH2061"]), file.path(hubCache(temp),
    'data42_21221_2.mzXML'));
    rtDevModelling(MS2Dir=hubCache(temp),nCores=2,runOrder=paste0(
    system.file("extdata",package="adductomicsR"),
    '/runOrder2.csv'), intStdPeakList=c(290.21, 403.30, 516.38,
    587.42,849.40, 884.92, 958.46, 993.97,1050.52, 1107.06, 1209.73,
    1337.79,1465.85))

[Package adductomicsR version 1.0.0 Index]