groupClosest: Group values with differences below threshold

In rformassspectrometry/MsFeatures: Functionality for Mass Spectrometry Features

Group values with differences below threshold

Description

Group values with a difference between them being smaller than a user defined threshold. This function uses the groupSimilarityMatrix() or the groupSimilarityMatrixTree() function to create groups with smallest differences between its members. Differences between all members of one group are below the user defined threshold maxDiff. This is a more stringent grouping than what groupConsecutive() performs leading thus to smaller groups (with smaller differences between its members).

Usage

groupClosest(x, maxDiff = 1, FUN = groupSimilarityMatrix, ...)

Arguments

x	numeric of values that should be grouped.
maxDiff	numeric(1) defining the threshold for difference between values in x to be grouped into the same group.
FUN	supported similarity calculation function. Can be either groupSimilarityMatrix (the default) or groupSimilarityMatrixTree, the latter being faster and less memory demanding.
...	additional parameters passed to FUN.

Value

integer with the group assignment (values grouped together have the same return value).

Author(s)

Johannes Rainer, Johan Lassen

See Also

Other grouping operations: groupConsecutive(), groupSimilarityMatrix(), groupSimilarityMatrixTree()

Examples

x <- c(1.1, 1.9, 2.2)
groupClosest(x)
## Although the difference between the 1st and 2nd element would be smaller
## than the threshold, they are not grouped because the difference between
## the 2nd and 3rd element is even smaller. The first element is also not
## put into the same group, because it has a difference > diffRt to the 3rd
## element.

x <- c(1.1, 1.5, 1.7, 2.3, 2.7, 4.3, 4.4, 4.9, 5.2, 5.4, 5.8, 6, 7,
    9, 9.5, 15)

groupClosest(x)

rformassspectrometry/MsFeatures documentation built on June 15, 2025, 12:55 a.m.