DEPRECATED: Extract a data.frame containing MS data

UPDATE: the extractMsData and plotMsData functions are deprecated and as(x, "data.frame") and plot(x, type = "XIC") (x being an OnDiskMSnExp or XCMSnExp object) should be used instead. See examples below. Be aware that filtering the raw object might however drop the adjusted retention times. In such cases it is advisable to use the applyAdjustedRtime() function prior to filtering.

Extract a data.frame of retention time, mz and intensity values from each file/sample in the provided rt-mz range (or for the full data range if rt and mz are not defined).

Usage

# S4 method for class 'OnDiskMSnExp'
extractMsData(object, rt, mz, msLevel = 1L)

# S4 method for class 'XCMSnExp'
extractMsData(
  object,
  rt,
  mz,
  msLevel = 1L,
  adjustedRtime = hasAdjustedRtime(object)
)

Arguments

object

A XCMSnExp or OnDiskMSnExp object.

rt

numeric(2) with the retention time range from which the data should be extracted.

mz

numeric(2) with the mz range.

msLevel

integer defining the MS level(s) to which the data should be sub-setted prior to extraction; defaults to msLevel = 1L.

adjustedRtime

(for extractMsData,XCMSnExp): logical(1) specifying if adjusted or raw retention times should be reported. Defaults to adjusted retention times, if these are present in object.

Value

A list of length equal to the number of samples/files in object. Each element being a data.frame with columns "rt", "mz" and "i" with the retention time, mz and intensity tuples of a file. If no data is available for the mz-rt range in a file a data.frame with 0 rows is returned for that file.

See also

XCMSnExp for the data object.

Author

Johannes Rainer

Examples

## Load a test data set with detected peaks
library(MSnbase)
data(faahko_sub)
## Update the path to the files for the local system
dirname(faahko_sub) <- system.file("cdf/KO", package = "faahKO")

## Disable parallel processing for this example
register(SerialParam())

## Extract the full MS data for a certain retention time range
## as a data.frame
tmp <- filterRt(faahko_sub, rt = c(2800, 2900))
ms_all <- as(tmp, "data.frame")
head(ms_all)
#>   file       rt    mz     i
#> 1    1 2800.284 200.1   968
#> 2    1 2800.284 201.0  1273
#> 3    1 2800.284 201.9  1729
#> 4    1 2800.284 203.0   859
#> 5    1 2800.284 205.0 24136
#> 6    1 2800.284 206.0  3913
nrow(ms_all)
#> [1] 79960