MALDIquant: match.closest – R documentation

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match.closest

Relaxed Value Matching

Description

match.closest returns a vector of the positions of (first) matches its first arguments in its second. In contrast to the similar match it just accept numeric arguments but has an additional tolerance argument that allows relaxed matching.

Usage

match.closest(x, table, tolerance = Inf, nomatch = NA_integer_)

Arguments

`x`	`numeric`, the values to be matched.
`table`	`numeric`, the values to be matched against. In contrast to `match` `table` has to be sorted in increasing order.
`tolerance`	`numeric`, accepted tolerance. Use `Inf` to match without restrictions. Could be of length one or the same length as `table`.
`nomatch`	`numeric`, if the difference between the value in `x` and `table` is larger than `tolerance` `nomatch` is returned. Has to be of length one.

Value

An integer vector of the same length as x giving the closest position in table of the first match or nomatch if there is no match.

Examples

library("MALDIquant")
match.closest(c(1.1, 1.4, 9.8), 1:10)
# [1]  1  1 10
match.closest(c(1.1, 1.4, 9.8), 1:10, tolerance=0.25)
# [1]  1 NA 10
match.closest(c(1.1, 1.4, 9.8), 1:10, tolerance=0.25, nomatch=0)
# [1]  1  0 10

## this function is most useful if you want to subset an intensityMatrix
## by a few (reference) peaks

## create an example intensityMatrix
im <- matrix(1:10, nrow=2, dimnames=list(NULL, 1:5))
attr(im, "mass") <- 1:5
im
#      1 2 3 4  5
# [1,] 1 3 5 7  9
# [2,] 2 4 6 8 10
# attr(,"mass")
# [1] 1 2 3 4 5

## reference peaks
ref <- c(2.2, 4.8)

im[, match.closest(ref, attr(im, "mass"), tolerance=0.25, nomatch=0)]
#      2  5
# [1,] 3  9
# [2,] 4 10

MALDIquant

Quantitative Analysis of Mass Spectrometry Data

v1.19.3

GPL (>= 3)

Authors

Sebastian Gibb [aut, cre] (<https://orcid.org/0000-0001-7406-4443>), Korbinian Strimmer [ths] (<https://orcid.org/0000-0001-7917-2056>)

Initial release

2019-05-12