readMgfData {MSnbase} | R Documentation

## Import mgf files as 'MSnExp' instances.

### Description

Reads a mgf file and generates an `"MSnExp"` object.

### Usage

    readMgfData(filename, pdata = NULL, centroided = TRUE, smoothed = FALSE,
    verbose = isMSnbaseVerbose(), cache = 1)

### Arguments

`filename` | character vector with file name to be read.
`pdata` | an object of class `"AnnotatedDataFrame"`.
`smoothed` | `Logical` indicating whether spectra already smoothed or not. Default is 'FALSE'. Used to initialise `"MSnProcess"` object in `processingData` slot.
`centroided` | `Logical` indicating whether spectra are centroided or not. Default is 'TRUE'. Used to initialise `"MSnProcess"` object in `processingData` slot.
`cache` | Numeric indicating caching level. Default is 1. Under development.
`verbose` | verbosity flag.

### Details

Note that when reading an mgf file, the original order of the spectra is lost. Thus, if the data was originally written to mgf from an `MSnExp` object using `writeMgfData`, although the feature names will be identical, the spectra are not as a result of the reordering. See example below.

### Value

An instance of

### Author(s)

Guangchuang Yu <guangchuangyu@gmail.com> and Laurent Gatto <lg390@cam.ac.uk>

### See Also

`writeMgfData` method to write the content of `"Spectrum"` or `"MSnExp"` objects to mgf files. Raw data files can also be read with the `readMSData` function.

### Examples

      data(itraqdata)
      writeMgfData(itraqdata, con="itraqdata.mgf", COM="MSnbase itraqdata")
      itraqdata2 <- readMgfData("itraqdata.mgf")
      ## note that the order of the spectra is altered
      ## and precision of some values (precursorMz for instance)
      match(signif(precursorMz(itraqdata2),4),signif(precursorMz(itraqdata),4))
      ## [1]  1 10 11 12 13 14 15 16 17 18 ...
      ## ... but all the precursors are there
      all.equal(sort(precursorMz(itraqdata2)),
                sort(precursorMz(itraqdata)),
                check.attributes=FALSE,
                tolerance=10e-5)
      ## is TRUE
      all.equal(as.data.frame(itraqdata2[[1]]),as.data.frame(itraqdata[[1]]))
      ## is TRUE
      all.equal(as.data.frame(itraqdata2[[3]]),as.data.frame(itraqdata[[11]]))
      ## is TRUE
      f <- dir(system.file(package="MSnbase",dir="extdata"),
               full.name=TRUE,
               pattern="test.mgf")
      (x <- readMgfData(f))
      x[[2]]
      precursorMz(x[[2]])
      precursorIntensity(x[[2]])
      precursorMz(x[[1]])
      precursorIntensity(x[[1]]) ## was not in test.mgf
      scanIndex(x)

[Package MSnbase version 2.12.0 Index]