matchRtMz: Match features based on their retention time and m/z values

In EuracBiomedicalResearch/CompMetaboTools: Utility Functions from the Eurac Research Computational Metabolomics Team

Match features based on their retention time and m/z values

Description

matchRtMz matches elements (features) in x with elements in table based on similarity of their m/z and retention time. With parameter duplicates = "closest", the function return the index of the best match, considering the m/z difference of features that are within the acceptable retention time difference (defined by rt_tolerance). With duplicates = "keep" the index of all matching rows in table are returned.

Usage

matchRtMz(
  x,
  table,
  nomatch = NA_integer_,
  rt_tolerance = 2,
  tolerance = 0,
  ppm = 20,
  duplicates = c("closest", "keep"),
  mzcol = "mz",
  rtcol = "rt"
)

Arguments

x	data.frame, matrix or DataFrame with feature definitions (i.e. m/z and retentin times) that should be matched against features in table.
table	data.frame, matrix or DataFrame with feature definitions to match features in x against.
nomatch	value that should be returned if no match for a feature is found.
rt_tolerance	numeric(1) with the largest acceptable difference in retention time.
tolerance	numeric(1) with a constant acceptable difference of m/z values for features to be considered matching.
ppm	numeric(1) with a m/z-dependent relative acceptable difference (in parts per million) of m/z values.
duplicates	character(1) whether the best (⁠duplicates = "closest", default) or all matches (⁠duplicates = "keep"') shpuld be returned.
mzcol	character(1) with the name of the column containing the m/z ratios.
rtcol	character(1) with the name of the column containing the retention times.

Value

for duplicates = "closest": integer of length equal to nrow(x) with the index of the row in table that matches each row in x (e.g. c(3, 4) means the first feature in x matches with the 3rd feature in table. For duplicates = "keep": list of length equal to nrow(x) with indices of all rows in table that match each row in x.

Note

The function first finds features in table with a difference of retention time which is smaller than rt_tolerance and matches these using the closest() function.

Author(s)

Johannes Rainer

Examples

x <- data.frame(mz = c(23.4, 45.6, 56.9, 76.5, 76.5, 76.5, 80.1),
    rt = c(12, 34, 59, 34, 67, 65, 67))

set.seed(123)
y <- rbind(x, x)
y$mz <- y$mz + rnorm(nrow(y), sd = 0.0002)
y$rt[1:nrow(x)] <- x$rt + 2
y <- y[order(y$mz), ]

matchRtMz(x, y)

## Keeping all matches
matchRtMz(x, y, duplicates = "keep")

## Lower ppm
matchRtMz(x, y, duplicates = "keep", ppm = 5)

## even lower
matchRtMz(x, y, duplicates = "keep", ppm = 2)

matchRtMz(x, y, ppm = 0)

EuracBiomedicalResearch/CompMetaboTools documentation built on Jan. 31, 2024, 1:14 p.m.