groupConsecutive: Grouping of sorted values into sets with smallest differences

In rformassspectrometry/MsFeatures: Functionality for Mass Spectrometry Features

Grouping of sorted values into sets with smallest differences

Description

groupConsecutive groups sorted values in x for which the difference is smaller than maxDiff. As a result, the mean difference between the groups will always be larger than maxDiff, but difference between individual values within the same group (e.g. between the first and last) can be larger maxDiff.

In detail, from the sorted x, the function starts from the smallest value defining the first group as the one containing all values in x with a difference to this first value which is ⁠<= maxDiff⁠. The next group is the defined based on the next larger value that is not part of the first group and includes all values with a difference ⁠<= maxDiff⁠ to this value. For values fulfilling this criteria but being already part of a previous group, the differences to the mean value of the current group and to the mean of previous groups are compared and values are assigned to the group to which they have the smallest difference.

Example: values ⁠1.1, 1.9, 2.2⁠ should be grouped with a maxDiff = 1. The first group is defined to include all values for which the difference to the first value (1.1) is smaller maxDiff. Thus, the first group is defined to contain values ⁠1.1 and 1.9⁠. Then the next group is defined based on the next larger value not part of any group, 2.2. This group contains values 1.9 and 2.2 with the value 1.9 being already assigned to the first group. The difference between this value 1.9 and the mean of the current group (⁠mean(c(1.9, 2.2)⁠) is then compared to the difference of 1.9 to the mean value of the group 1.9 is already part of (which is mean(c(1.1, 1.9))). Since the difference to the second group is smaller, 1.9 is removed from the first group and assigned to the second one.

Usage

groupConsecutive(x, maxDiff = 1)

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.

Value

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

Note

The difference between consecutive (ordered) values within a defined group is always ⁠<= maxDiff⁠, but the difference between e.g. the first and the last of the (ordered) values can be larger than maxDiff. See groupClosest() for a more stringent grouping function.

Author(s)

Johannes Rainer

See Also

Other grouping operations: groupClosest(), groupSimilarityMatrix()

Examples

## The example described above
x <- c(1.1, 1.9, 2.2)
groupConsecutive(x)

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)

groupConsecutive(x)
## value 5.2 was initially grouped with 4.3 (because their difference is
## smaller 1, but then re-grouped together with 5.4 because the difference
## between 5.4 (the next value outside the group of 4.3) and 5.2 is smaller
## than its difference to the mean value of the group for value 4.3

## Example for a case in which values are NOT grouped into the same group
## even if the difference between them is <= maxDiff
a <- c(4.9, 5.2, 5.4)
groupConsecutive(a, maxDiff = 0.3)

rformassspectrometry/MsFeatures documentation built on April 21, 2023, 6:20 a.m.