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

table 

nomatch 
value that should be returned if no match for a feature is found. 
rt_tolerance 

tolerance 

ppm 

duplicates 

mzcol 

rtcol 

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
.
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.
Johannes Rainer
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)
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