xcmsSet-utils: Various utility functions for xcmsSet objects

In jotsetung/xcmsExtensions: Extensions to the xcms package

Description

These functions provide additional functionality for xcmsSet objects from the xcms package.

Usage

## S4 method for signature 'xcmsSet'
peakGroupSummary(object, class, value="into")

visualizeXcmsSet(...)

Arguments

(in alphabetic order)

class	For peakGroupSummary: optional factor specifying groups of samples for which the summary should be performed. If not specified (the default) the factor returned by the sampclass method is used, i.e. peak group summaries are calculated for each sample class.
object	An xcmsSet object.
value	For peakGroupSummary: character string specifying the value on which the summary should be calculated. Defaults to "into", i.e. summary is calculated on the original (raw) peak area (intensity). See groupval method for xcmsSet objects for more information.
...	Presently not used.

Value

Refer to the method and function description above for detailed information on the returned result object.

Data visualization

visualizeXcmsSet

This function starts the shiny app to visualize xcmsSet objects present in the current workspace.

Data summaries and quality controls

peakGroupSummary

Calculates and returns peak group summaries, i.e. the minimal, maximal and mean intensity, the RSD (relative standard deviation of coefficient of variationy) and the proportion of samples in which the peak was identified. These summaries are calculated for groups of samples specified with the class argument, which defaults to the classes defined in the xcmsSet (returned by the sampclass method).

The method returns a matrix, each row representing a peak group, with columns "minInt", "maxInt", "meanInt", "RSD" and "propPresent" for each of the sample classes. The ordering of the rows corresponds to the ordering of peak groups returned by the groupval or groups methods.

Author(s)

Johannes Rainer.

See Also

MSdata, MSslice, MSsliceList

jotsetung/xcmsExtensions documentation built on May 19, 2019, 9:42 p.m.