LOB_RTFsort: Screen annoations against standards retention time factors...
In hholm/LOB_tools: Additional Data Screening And Cleaning Tools For LOBSTAHS

View source: R/LOB_RTFsort.R

LOB_RTFsort

R Documentation

Screen annoations against standards retention time factors and previous MS2 verifications.

Description

This function allows the user screen lipid annotations against known retention time factors (RTFs), that is the ratio between the lipids retention time and a standards retention time. While retention times in LC-MS may have large shifts, RTFs are largely fixed as peaks usually drift in similar directions with instrument changes. Thus, RTFs provide a metric of retention time consitancy that may be used between datasets for identify compounds repeatably.

Usage

LOB_RTFsort(peakdata, RT_Factor_Dbase, choose_class = NULL, 
            plot_data = FALSE, save_plots = FALSE, data_title)

Arguments

`peakdata`	A object of class `LOBSet` or `data.frame` generated with `getLOBpeaklist()` that contains the peakdata of identifed lipids.
`RT_Factor_Dbase`	A `data.frame` containing standard information and RTFs.
`choose_class`	A `vector` of classes in the peakdata that should be screened. If NULL all classes are screened.
`plot_data`	A `logical` indicating whether the data should be plotted (TRUE) or should not be (FALSE).
`save_plots`	A `logical` indicating whether the plots should be saved (TRUE) or should not be (FALSE) to the current working directory.
`data_title`	NA

Value

Returns a data.frame or a LOBSet object matching the peakdata argument but with columns containing RTF screening data appended. When run on a LOBSet object this screening information appended to the data.frame in the @peakdata slot of the object. The column names are as follows:

`DNPPE_Factor`	RTF for the annotation: The retention time of the peakgroup in question divided by the retention time of DNP-PE.
`DBase_DNPPE_RF`	Database RTF for this annotation: A previously observed RTF for this annotation.
`Flag`	A flag denoting how close the actual RTF is too the database value. If the two values are within 5% of eachother the tag "5%_rtv" is used. Also, if an appropriate MS2 spectra for this compound has been seen at this RTF previously, then it receives the tag "ms2v". If the peakgroup is within 5-10% of the database RTF than it is given the tag "10%_rtv". If the RTF is greater than 10% removed from the database value it is given the tag "Red". A tag of "Unknown" is given to every peakgroup for which there is no database value.

Note

Currently in development.

Author(s)

Henry Holm, hholm@mit.edu
Dan Lowenstien, dlowenstein@whoi.edu
Max Jahns, mjahns@mit.edu
Shavonna Bent, sbent@mit.edu

Examples

# Screen a LOBSet
LOBSet <- PtH2O2lipids::ptH2O2lipids$LOBSet
LOB_RTFsort(LOBSet, RT_Factor_Dbase, choose_class = NULL, plot_data = TRUE, save_plots = FALSE, data_title)

hholm/LOB_tools documentation built on Jan. 28, 2024, 12:08 p.m.