Representation of Spectra matches

Matches between query and target spectra can be represented by the MatchedSpectra object. Functions like the matchSpectra() function will return this type of object. By default, all data accessors work as left joins between the query and the target spectra, i.e. values are returned for each query spectrum with eventual duplicated entries (values) if the query spectrum matches more than one target spectrum.

Usage

MatchedSpectra(
  query = Spectra(),
  target = Spectra(),
  matches = data.frame(query_idx = integer(), target_idx = integer(), score = numeric())
)

# S4 method for class 'MatchedSpectra'
spectraVariables(object)

# S4 method for class 'MatchedSpectra'
queryVariables(object)

# S4 method for class 'MatchedSpectra'
targetVariables(object)

# S4 method for class 'MatchedSpectra'
colnames(x)

# S4 method for class 'MatchedSpectra'
x$name

# S4 method for class 'MatchedSpectra'
spectraData(object, columns = spectraVariables(object))

# S4 method for class 'MatchedSpectra'
matchedData(object, columns = spectraVariables(object), ...)

# S4 method for class 'MatchedSpectra'
addProcessing(object, FUN, ..., spectraVariables = character())

# S4 method for class 'MatchedSpectra'
plotSpectraMirror(
  x,
  xlab = "m/z",
  ylab = "intensity",
  main = "",
  scalePeaks = FALSE,
  ...
)

# S4 method for class 'MatchedSpectra,MsBackend'
setBackend(object, backend, ...)

Arguments

query: Spectra with the query spectra.
target: Spectra with the spectra against which query has been matched.
matches: data.frame with columns "query_idx" (integer), "target_idx" (integer) and "score" (numeric) representing the n:m mapping of elements between the query and the target Spectra.
object: MatchedSpectra object.
x: MatchedSpectra object.
name: for $: the name of the spectra variable to extract.
columns: for spectraData: character vector with spectra variable names that should be extracted.
...: for addProcessing: additional parameters for the function FUN. For plotSpectraMirror: additional parameters passed to the plotting functions.
FUN: for addProcessing: function to be applied to the peak matrix of each spectrum in object. See Spectra() for more details.
spectraVariables: for addProcessing: character with additional spectra variables that should be passed along to the function defined with FUN. See Spectra() for details.
xlab: for plotSpectraMirror: the label for the x-axis.
ylab: for plotSpectraMirror: the label for the y-axis.
main: for plotSpectraMirror: an optional title for each plot.
scalePeaks: for plotSpectraMirror: logical(1) if peak intensities (per spectrum) should be scaled to a total sum of one (per spectrum) prior to plotting.
backend: for setBackend: instance of an object extending MsBackend. See help for setBackend in Spectra() for more details.

Value

See individual method desciption above for details.

Creation, subset and filtering

MatchedSpectra objects are the result object from the matchSpectra(). While generally not needed, MatchedSpectra objects can also be created with the MatchedSpectra function providing the query and target Spectra objects as well as a data.frame with the matches between query and target elements. This data frame is expected to have columns "query_idx", "target_idx" with the integer indices of query and target objects that are matched and a column "score" with a numeric score for the match.

MatchedSpectra objects can be subset using:

[ subset the MatchedSpectra selecting query spectra to keep with parameter i. The target spectra will by default be returned as-is.
pruneTarget cleans the MatchedSpectra object by removing non-matched target spectra.

In addition, MatchedSpectra can be filtered with any of the filtering approaches defined for Matched() objects: SelectMatchesParam(), TopRankedMatchesParam() or ScoreThresholdParam().

Extracting data

$ extracts a single spectra variable from the MatchedSpectra x. Use spectraVariables to get all available spectra variables. Prefix "target_" is used for spectra variables from the target Spectra. The matching scores are available as spectra variable "score". Similar to a left join between the query and target spectra, this function returns a value for each query spectrum with eventual duplicated values for query spectra matching more than one target spectrum. If spectra variables from the target spectra are extracted, an NA is reported for query spectra that don't match any target spectra. See examples below for more details.
length returns the number of query spectra.
matchedData same as spectraData below.
query returns the query Spectra.
queryVariables returns the spectraVariables of query.
spectraData returns spectra variables from the query and/or target Spectra as a DataFrame. Parameter columns allows to define which variables should be returned (defaults to columns = spectraVariables(object)), spectra variable names of the target spectra need to be prefixed with target_ (e.g. target_msLevel to get the MS level from target spectra). The score from the matching function is returned as spectra variable "score". Similar to $, this function performs a left join of spectra variables from the query and target spectra returning all values for all query spectra (eventually returning duplicated elements for query spectra matching multiple target spectra) and the values for the target spectra matched to the respective query spectra. See help on $ above or examples below for details.
spectraVariables returns all available spectra variables in the query and target spectra. The prefix "target_" is used to label spectra variables of target spectra (e.g. the name of the spectra variable for the MS level of target spectra is called "target_msLevel").
target returns the target Spectra.
targetVariables returns the spectraVariables of target (prefixed with "target_").
whichTarget returns an integer with the indices of the spectra in target that match at least on spectrum in query.
whichQuery returns an integer with the indices of the spectra in query that match at least on spectrum in target.

Data manipulation and plotting

addProcessing: add a processing step to both the query and target Spectra in object. Additional parameters for FUN can be passed via .... See addProcessing documentation in Spectra() for more information.
plotSpectraMirror: creates a mirror plot between the query and each matching target spectrum. Can only be applied to a MatchedSpectra with a single query spectrum. Setting parameter scalePeaks = TRUE will scale the peak intensities per spectrum to a total sum of one for a better graphical visualization. Additional plotting parameters can be passed through ....
setBackend: allows to change the backend of both the query and target Spectra() object. The function will return a MatchedSpectra object with the query and target Spectra changed to the specified backend, which can be any backend extending MsBackend.

Author

Johannes Rainer

Examples


## Creating a dummy MatchedSpectra object.
library(Spectra)
df1 <- DataFrame(
    msLevel = 2L, rtime = 1:10,
    spectrum_id = c("a", "b", "c", "d", "e", "f", "g", "h", "i", "j"))
df2 <- DataFrame(
    msLevel = 2L, rtime = rep(1:10, 20),
    spectrum_id = rep(c("A", "B", "C", "D", "E"), 20))
sp1 <- Spectra(df1)
sp2 <- Spectra(df2)
## Define matches between query spectrum 1 with target spectra 2 and 5,
## query spectrum 2 with target spectrum 2 and query spectrum 4 with target
## spectra 8, 12 and 15.
ms <- MatchedSpectra(
    sp1, sp2, matches = data.frame(query_idx = c(1L, 1L, 2L, 4L, 4L, 4L),
                                   target_idx = c(2L, 5L, 2L, 8L, 12L, 15L),
                                   score = 1:6))

## Which of the query spectra match at least one target spectrum?
whichQuery(ms)
#> [1] 1 2 4

## Extracting spectra variables: accessor methods for spectra variables act
## as "left joins", i.e. they return a value for each query spectrum, with
## eventually duplicated elements if one query spectrum matches more than
## one target spectrum.

## Which target spectrum matches at least one query spectrum?
whichTarget(ms)
#> [1]  2  5  8 12 15

## Extracting the retention times of the query spectra.
ms$rtime
#>  [1]  1  1  2  3  4  4  4  5  6  7  8  9 10

## We have duplicated retention times for query spectrum 1 (matches 2 target
## spectra) and 4 (matches 3 target spectra). The retention time is returned
## for each query spectrum.

## Extracting retention times of the target spectra. Note that only retention
## times for target spectra matching at least one query spectrum are returned
## and an NA is reported for query spectra without matching target spectrum.
ms$target_rtime
#>  [1]  2  5  2 NA  8  2  5 NA NA NA NA NA NA

## The first query spectrum matches target spectra 2 and 5, thus their
## retention times are returned as well as the retention time of the second
## target spectrum that matches also query spectrum 2. The 3rd query spectrum
## does match any target spectrum, thus `NA` is returned. Query spectrum 4
## matches target spectra 8, 12, and 15, thus the next reported retention
## times are those from these 3 target spectra. None of the remaining 6 query
## spectra matches any target spectra and thus `NA` is reported for each of
## them.

## With `queryIndex` and `targetIndex` it is possible to extract the indices
## of the matched query-index pairs
queryIndex(ms)
#> [1] 1 1 2 4 4 4
targetIndex(ms)
#> [1]  2  5  2  8 12 15

## The first match is between query index 1 and target index 2, the second
## match between query index 1 and target index 5 and so on.
## We could use these indices to extract a `Spectra` object containing only
## matched target spectra and assign a spectra variable with the indices of
## the query spectra
matched_target <- target(ms)[targetIndex(ms)]
matched_target$query_index <- queryIndex(ms)

## This `Spectra` object thus contains information from the matching, but
## is a *conventional* `Spectra` object that could be used for further
## analyses.

## `spectraData` can be used to extract all (or selected) spectra variables
## from the object. Same as with `$`, a left join between the specta
## variables from the query spectra and the target spectra is performed. The
## prefix `"target_"` is used to label the spectra variables from the target
## spectra. Below we extract selected spectra variables from the object.
res <- spectraData(ms, columns = c("rtime", "spectrum_id",
    "target_rtime", "target_spectrum_id"))
res
#> DataFrame with 13 rows and 4 columns
#>         rtime spectrum_id target_rtime target_spectrum_id
#>     <integer> <character>    <integer>        <character>
#> 1           1           a            2                  B
#> 2           1           a            5                  E
#> 3           2           b            2                  B
#> 4           3           c           NA                 NA
#> 5           4           d            8                  C
#> ...       ...         ...          ...                ...
#> 9           6           f           NA                 NA
#> 10          7           g           NA                 NA
#> 11          8           h           NA                 NA
#> 12          9           i           NA                 NA
#> 13         10           j           NA                 NA
res$spectrum_id
#>  [1] "a" "a" "b" "c" "d" "d" "d" "e" "f" "g" "h" "i" "j"
res$target_spectrum_id
#>  [1] "B" "E" "B" NA  "C" "B" "E" NA  NA  NA  NA  NA  NA 

## Again, all values for query spectra are returned and for query spectra not
## matching any target spectrum NA is reported as value for the respecive
## variable.

## The example matched spectra object contains all query and all target
## spectra. Below we subset the object keeping only query spectra that are
## matched to at least one target spectrum.
ms_sub <- ms[whichQuery(ms)]

## ms_sub contains now only 3 query spectra:
length(query(ms_sub))
#> [1] 3

## while the original object contains all 10 query spectra:
length(query(ms))
#> [1] 10

## Both object contain however still the full target `Spectra`:
length(target(ms))
#> [1] 200
length(target(ms_sub))
#> [1] 200

## With the `pruneTarget` we can however reduce also the target spectra to
## only those that match at least one query spectrum
ms_sub <- pruneTarget(ms_sub)
length(target(ms_sub))
#> [1] 5