sgibb/maldiquantforeign

Import/Export routines for MALDIquant

maldiquantforeign's Issues

unitAccession not followed by unitName

Hi, in this cvParam only the unitAccession is given, but the unitName is not given; please consider adding unitName="number of counts" to the function in line 329 to make it valid mzML

MALDIquantForeign/R/mzMl-functions.R

Lines 326 to 329 in 4c6b47f

	.writeXmlTag("cvParam", intend=3, file=file,
	attrs=c(cvRef="MS", accession="MS:1000515",
	name="intensity array", unitCvRef="MS",
	unitAccession="MS:1000131"))

Error when skipping lines in text file

Hi,
Thanks for this package.
I guess that the beginning of the code L24-L35 is guessing the right parameters for read.table. But then read.table L38 is not applied to the raw file but to already processed text lines. Because skipping lines already took place, it should not be applied twice. I think that the file name actually should be given to read.table L38 instead of the text variable.
Best.

MALDIquantForeign/R/importTab-functions.R

Lines 24 to 39 in 37fbb16

	text <- readLines(file, encoding=encoding)
	text <- tail(text, length(text) - skip)
	text <- text[!startsWith(trimws(text), comment.char)]
	if (is.null(sep)) {
	sep <- .autoSep(text)
	}
	if (is.null(header)) {
	header <- .autoHeader(text, sep=sep)
	}
	## load ms file
	s <- read.table(text=text, header=header, sep=sep, skip=skip,
	comment.char=comment.char, stringsAsFactors=FALSE, ...)

add missing "usage" entry for export methods in man pages

install_github(username="klutometis", repo="roxygen", ref="s4")

.writeImzMlDocument doesn't pass the 'processed' argument to .addIbdOffsets

In the .writeImzMlDocument function, .addIbdOffsets gets called without the processed argument, leading to .addIbdOffsets using always the default (=TRUE). Subsequently, a wrong imzml file is created,
which makes the exported data unusable.
Original function:

.writeImzMlDocument <- function(x, file,
                                id=.withoutFileExtension(basename(file)),
                                processed=TRUE, uuid=.uuid(),
                                coordinates=MALDIquant::coordinates(x),
                                pixelSize=c(metaData(x[[1L]])$imaging$pixelSize,
                                            100, 100)[1L:2L], ...) {

...

  .writeMzMlDocument(x=.addIbdOffsets(x), file=file, id=id,
                     imsArgs=list(uuid=uuid, sha1=sha1, processed=processed),
                     ...)
}

Suggested fix:

.writeImzMlDocument <- function(x, file,
                                id=.withoutFileExtension(basename(file)),
                                processed=TRUE, uuid=.uuid(),
                                coordinates=MALDIquant::coordinates(x),
                                pixelSize=c(metaData(x[[1L]])$imaging$pixelSize,
                                            100, 100)[1L:2L], ...) {

...

  .writeMzMlDocument(x=.addIbdOffsets(x, processed=processed), file=file, id=id,
                     imsArgs=list(uuid=uuid, sha1=sha1, processed=processed),
                     ...)
}

Import centroided data as MassPeaks

mzXML and mzML have a flag for centroided data.
For all other formats an argument centroided=TRUE or a function asMassPeaks would be fine.

add Ciphergen XML support

add mzML export methods

http://www.psidev.info/mzml_1_0_0
http://www.peptideatlas.org/tmp/mzML1.1.0.html
http://psidev.cvs.sourceforge.net/*checkout*/psidev/psi/psi-ms/mzML/controlledVocabulary/psi-ms.obo

Unable to write imzML files via exportImzMl

exportImzMl complains when attempting writing to an imzML file, here is a reproducible example (file attached
massPeaksList.gz ):

s <- readRDS(file = "massPeaksList.gz")
MALDIquantForeign::exportImzMl(x = s, path = "test.imzML", processed = TRUE)

Error in get(as.character(FUN), mode = "function", envir = envir) : 
  object 'coordinates<-' of mode 'function' was not found
  
packageVersion("MALDIquantForeign")
[1] ‘0.12’

The issue is resolved when explicitly loading MALDIquant into the environment. The issue appears to be in .writeImzMlDocument function in imzMl-functions.R line #48 coordinates(x) <- coordinates, the function coordinates is called without specifying MALDIquant package namespace.

Also the documentation of ?MALDIquantForeign::exportImzMl says the the input should be "a MassSpectrum object or a list of MassSpectrum objects" but it didn't have any issues exporting a list of MassPeaks objects (the attached file).

Replace `downloader::download` by `base::download.file`

Since R 3.2.2 download.file supports HTTPS, so downloader::download is not needed anymore.

download is always "verbose"

.download doesn't respect verbose=FALSE

add exporter for imzML files

Integrate `mzR` as additional backend for mz(X)ML

Warning when exporting imzML and faulty imzML

I want to export some IMS data as imzML file with the exportImzMl function. During the process I get the following warning:
Warning message:
In .ibdOffsets(x, processed = processed, encodedLengthSize = encodedLengthSize) :
integer overflow in 'cumsum'; use 'cumsum(as.numeric(.))'
The resulting imzML file has "NA" value for most of the "external offset" entries. Additionally, even with processed=FALSE the external offset value in mzArray is always a different value, while it should be the, if I understood it correctly.
The data set, that I want to convert, is relatively large (7953 spectra, 36713 data points each, around 3 GB object size).

MALDIquantForeign generates and prints a warning for every spectrum when reading imzML

I have been evaluating multiple imzML parsers (see here https://imzml.github.io/) with publicly available imzML datasets (e.g. https://metaspace2020.eu/datasets?ds=2017-06-30_07h26m26s) and experienced some issues with MALDIquantForeign.

It seems that if a common 'error' is encountered for each spectrum, then this will flood the console with one message per spectrum (which for MSI Data is a lot!) eventually leading to a system crash. The error for the dataset linked above is given below. Perhaps it would be possible to just display the warning once per dataset, rather than per spectrum?

- Warning in .createMassObject(mass = mass, intensity = intensity, metaData = m, :
-    According to the metadata information the imported data are centroided, but they are treated as profile (MassSpectrum) data. Maybe you want to use 'centroided=TRUE'. See '?import' for details.

parallel support

Parsing XML files takes longer than reading them. So all XML parsing import functions could benefit from parallelization.

fix methods NOTE

Package in Depends field not imported from: ‘methods’
These packages needs to imported from for the case when
this namespace is loaded but not attached.
See the information on DESCRIPTION files in the chapter ‘Creating R
packages’ of the ‘Writing R Extensions’ manual.

move tests

testthat 0.8 comes with a new recommended structure for storing your tests. To
better meet CRAN recommended practices, testthat now recommend that you to put
your tests in tests/testthat, instead of inst/test (this makes it
possible for users to choose whether or not to install tests). With this
new structure, you'll need to use test_check() instead of test_packages()
in the test file (usually tests/testthat.R) that runs all testthat unit
tests.

add importer for msd files

Reading/Converting Bruker's MALDI-FTICR .d file

Hi Sebastian,

I would like to use MALDIQuant to analyse Bruker's MALDI-FTICR data. But I don't know how do I convert the raw file to mzML file or other MALDIquantForeign supported format. Or will MALDIquantForeign support such data type?

Here I upload a compressed sample data. The acquired data is basically a folder, which contains various files in it. It can be opened with Bruker's DataAnalysis software, and can be exported to, for instance, .xml or .ascii file. But the software does not support exporting to mzML format.

Here I attached one example data, could you please help?
WT.d.zip

Thanks a lot.

Dong

add possibility to ignore specific path/files

It would be useful to avoid importing of some files (e.g. Bruker LIFT files or calibration runs):

Maybe an ignorePattern argument should be added to import.

Typical directory tree (we want only import 0_L19/1SRef/fid and ignore all *LIFT/1SRef/fid files):

├── 0_L19
│   │   └── 1
│   │       ├── 1247.4076.LIFT
│   │       │   └── 1SRef
│   │       │       ├── acqu
│   │       │       ├── acqus
│   │       │       ├── fid
│   │       │       └── sptype
│   │       ├── 1290.4581.LIFT
│   │       │   └── 1SRef
│   │       │       ├── acqu
│   │       │       ├── acqus
│   │       │       ├── fid
│   │       │       └── sptype
│   │       ├── 1SRef
│   │       │   ├── acqu
│   │       │   ├── acqus
│   │       │   ├── fid
│   │       │   └── sptype
│   │       ├── 2089.7704.LIFT
...

comment.char is ignored in .autoSep

Importing CSV files with comments currently fails because .autoSep and .autoHeader don't know comment.char and ignore it.

avoid false-positive match of xml files by autoimporter

• Don't count every xml file as Ciphergen XML file. (look for <spectrum> tag?)

Error when reading Analyze7.5 files

Hi,
I am wondering if this check can be relaxed or changed into a warning:
if (size != 348 && size != 384) { stop(sQuote(filename), " is no ANALYZE header file.") }
I have some Analyze7.5 files that do not match this size requirement but work for example in Cardinal.
Thanks,
Melanie

access specific spectra by their x, y coordinates within an imzML file

add argument 'filterEmptySpectra' to import

We should add an argument filterEmptySpectra (default: TRUE) to import to avoid problems with empty spectra in downstream analysis in MALDIquant.

Must this package depend on R>=3.2.2 ?

Hello,

I'm puzzled as to why MALDIquant can work with R>=3.2.0 but MALDIquantForeign depends on R>=3.2.2. If this is not necessary, please amend MALDIquantForeign to depend on R>=3.2.0

many thanks,

Simon

add compression support for import

add unpacking support forthe following file types: zip, tar, gz,bz2, xz, lzma