ms.filter: Flexible interactive filtering of components and/or peaks via...

In nontarget: Detecting Isotope, Adduct and Homologue Relations in LC-MS Data

Description

Mark peaks and components in plots of retention time, m/z, mass defect or peak intensity. Select components or peaks by drawing a polygon.

Usage

ms.filter(component, x = "mz", y = "dm", xlim = FALSE, 
ylim = FALSE, rm.comp = FALSE, plot.comp = TRUE, 
rm.noncomp = TRUE, select.polygon = "inside", res = 100, 
filter.for = "raw")

Arguments

component	List of type comp generated by combine.
x	Scale of x-axis, any of "mz" (m/z), "dm" (mass defect), "rt" (retention time) or "int" (intensity).
y	Scale of y-axis, any of "mz" (m/z), "dm" (mass defect), "rt" (retention time) or "int" (intensity).
xlim	xlim=c(upper bound,lower bound), default = FALSE.
ylim	ylim=c(upper bound,lower bound), default = FALSE.
rm.comp	Select (i.e. remove) peaks assigned to components by combine?
plot.comp	Highlight peaks part of a component (red)?
rm.noncomp	Select (i.e. remove) peaks not assigned to components by combine?
select.polygon	Select peaks and/or components to be excluded "inside" or "outside" of the polygon drawn?
res	Resolution of polygon selection; increase if problems with selection by complicated polygons or along polygon boarder occur. Otherwise, ignore.
filter.for	What should be filtered and subsequently returned as value by the polygon selection? Any of "raw" (raw data, i.e. peak list), "pattern" (isotope pattern peak relations, i.e. subset of first entry in list of type pattern generated by pattern.search) or "adduct" (adduct relations, i.e. subset of first entry in list of type adduct generated by adduct.search)

Details

Selection refers to those peaks and/or components to be excluded. If not all peaks in the data set are assigned to components, they are still plotted and can thus e.g. be separated from those assigned to components by setting rm.comp vs. rm.noncomp.

Value

See filter.for argument. Either raw data (i.e. peak list), isotope pattern peak relations, (i.e. subset of first entry in list of type pattern generated by pattern.search) or adduct relations (i.e. subset of first entry in list of type adduct generated by adduct.search).

Note

Here, mass defect is defined as the difference of m/z to the nearest integer from rounding. rm.comp = FALSE and rm.noncomp = FALSE leads to no selection and thus no exclusions of anything.

Author(s)

Martin Loos

See Also

plotcomp combine

nontarget documentation built on May 2, 2019, 2:32 a.m.