LOB_genalg: Annotation selection based on retention time patterns using...
In hholm/LOB_tools: Additional Data Screening And Cleaning Tools For LOBSTAHS

LOB_genalg

R Documentation

Annotation selection based on retention time patterns using Genetic Algorythms

Description

This function allows the user screen lipid annotations based on their retention time patterns.

Usage

LOB_genalg <- function(peakdata, choose_class = NULL, save.files = FALSE,
                       plot_data = FALSE, use_ms2 = TRUE, hijacking = FALSE,
                       iters = 300, mutationChance = 0.01, elitism = T, popSize = 300)

Arguments

`peakdata`	A object of class `LOBSet` or `data.frame` generated with `getLOBpeaklist()` that contains the peakdata of identifed lipids.
`choose_class`	A `vector` of class `character` continaing lipid classes from the peakdata that should be screened. If NULL all lipid classes are screened.
`plot_data`	A `logical` indicating whether the data should be plotted (TRUE) or should not be (FALSE).
`save.files`	A `logical` indicating whether the plots should be saved (TRUE) or should not be (FALSE) to the current working directory.
`use_ms2`	A `logical` indicating whether each class should be prescreened based on MS2 verified peaks. The `LOB_RTFsort` function must be first used to flag annotations.
`hijacking`	A `logical` indicating whether....
`iters`	A single numeric `vector` passed to `genalg::rbga.bin` indicating the number of interations the genetic algorythm should run. If a stable soultion is no reached with defualt value this can be increased. Likewise, decreasing this value should improve run time. Solution evolution over interations can be monitored with `plot_data = TRUE`.
`popSize`	A single numeric `vector` indicating the population size in genetic algorythm simulations.

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

References

Need to put references to the literature/web site here

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. 10, 2025, 7:14 p.m.