adductomicsR: Processing of adductomic mass spectral datasets

Description Usage Arguments Value Examples

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

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)

`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.

LOESS RT models as adductSpectra AdductSpec object

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))