screen.homol: Screen EICs for Homologue Series
In schymane/ReSOLUTION: SOLUTIONS for High ReSOLUTION Mass Spectrometry

Description Usage Arguments Value Author(s) See Also Examples

This is a wrapper for plotEICs designed for screening homologue series built from build.homol.

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screen.homol(file, file_desc, series, series_name, adduct, rt_window=NULL, ppm=10,
greyscale=FALSE, smiles="", formula=NULL, addMSMS=FALSE, isLog=FALSE,
isPos=TRUE, kekulise=TRUE, writePDF=FALSE, writeCSV=FALSE)

`file`	Path and filename to mz(X)ML file to screen
`file_desc`	Description for the file (used in plot title and file names)
`series`	The series from `build.homol` to screen
`series_name`	The name of the series (used in legend)
`adduct`	The adduct species of the homologue to screen. NOTE: the adduct must be exactly as written in the adducts table in the enviPat package.
`rt_window`	The retention time window (in seconds) for EIC extraction. This is added to `rt` to form the extraction window. Should not be zero! If `NULL`, the whole EIC is extracted.
`ppm`	The ppm limit for EIC extraction
`greyscale`	If `TRUE`, greyscale plot will be produced. If `FALSE`, rainbow colours are assigned automatically.
`smiles`	SMILES code of the compound of interest. Can also be generic SMILES (this needs to be tested...).
`formula`	A text field to put the formula of the series if no SMILES.
`addMSMS`	Indicates whether MSMS scans should be added to plot with default settings `TRUE`. `FALSE` does not attempt to add MSMS scans.
`isLog`	If `TRUE`, EICs are plotted with a log scale; `FALSE` with absolute intensities. Zero intensities are lost with `TRUE`. TRUE may not work properly.
`isPos`	Setting to pass on to `plotEICs`. `TRUE` indicates positive mode; `FALSE` negative mode. Only relevant for switching data.
`kekulise`	Controls aromaticity detection in SMILES for plotting.
`writePDF`	Writes the plot to PDF rather than active device. PDF name is autocreated.
`writeCSV`	Writes the screen summary to CSV - file name is autocreated.

Returns a plot in the active device, or PDF and summary output.

Emma Schymanski <emma.schymanski@uni.lu>

plotEICs, build.homol

pegs <- build.homol("C4H10O3","C2H4O","PEGS",2,14)
library(RMassBank)
library(RMassBankData)
RmbDefaultSettings()
mzML_files <- list.files(system.file("spectra", package="RMassBankData"), ".mzML", full.names = TRUE)
mzML_file <- mzML_files[1]
screen.homol(mzML_file, "test_file", pegs, "PEGS_MpH", "M+H")
screen.homol(mzML_file, "test_file", pegs, "PEGS_MpNH4", "M+NH4")
#Note this doesn't look pretty as PEGS aren't present, but does test that it works.