trimAnnotation: Select a Subset of Annotated Peaks for Plotting
In schymane/ReSOLUTION: SOLUTIONS for High ReSOLUTION Mass Spectrometry

Description Usage Arguments Details Value Author(s) See Also Examples

This uses the filterPeakSatellites of RMassBank to select annotated peaks for plotting and thus prevent overlap.

1 2	trimAnnotation(annotated_dataframe,mzLimit=10,IntLimit=1, column_names = c("mz","anno","intensity","relInt"), UseRmbDefaultSettings=TRUE)

`annotated_dataframe`	The data frame containing the annotated data to trim
`mzLimit`	The `mz` window to exclude other annotations.
`IntLimit`	The default value of 1 is recommended. See details.
`column_names`	This should be used to defined the column names and can be retrieved from `annotated_dataframe` using `colnames`. NOTE that the columns `mz` and `intensity` MUST exist for this function to work.
`UseRmbDefaultSettings`	The default `TRUE` calls `RmbDefaultSettings`; if other settings are in use set this to `FALSE`. See Details.

UseRmbDefaultSettings: If RMassBank is not in use for any other purpose, the default TRUE calls RmbDefaultSettings to ensure that settings are present for use. If other settings have been defined using RMassBank, set this to FALSE to avoid overwriting those settings. This function retrieves settings and adjusts them internally without overwriting any stored settings. IntLimit: This is used in filterPeakSatellites and is relative to 1. For this context, this should be kept at 1. Values below 1 will let additional peaks through; values above 1 lead to strange behaviour.

Returns a "trimmed" annotated_dataframe

Emma Schymanski <emma.schymanski@uni.lu>

extractMS1.RMBarchive

MBrecord <- system.file("extdata","EA000405.txt",package="ReSOLUTION")
MBrecord <- system.file("extdata","EA026206_Simazine.txt",package="ReSOLUTION")
anno_peaks <- getMBPeaksAnnos(MBrecord, fixColNames=TRUE)
anno_cols <- sub("Int","intensity",colnames(anno_peaks))
colnames(anno_peaks) <- anno_cols
trimAnnotation(anno_peaks, mzLimit=10, IntLimit=1, column_names=anno_cols)