8000 mzTab import · Issue #92 · statOmics/MSqRob · GitHub
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cdlawless opened this issue Feb 5, 2021 · 1 comment
Open

mzTab import #92

cdlawless opened this issue Feb 5, 2021 · 1 comment

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@cdlawless
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Hi,

I've been using PD for the data processing and have exported the mzTab to use with MSqRob.
However, the function import2MSnSet returns an empty MSnSet object.

peptides<-import2MSnSet("path_to_mzTab", filetype = "mzTab")
>head(exprs(peptidesMatt))
1
2
3
4
5
6
>head(fData(peptides))
data frame with 0 columns and 311920 rows

I've checked the R code for import2MSnSet function for mzTab is selects:

} else if(filetype=="mzTab"){
    peptides <- read2MSnSet(file=file, pattern="peptide_abundance_study_variable", remove_pattern=remove_pattern, sep="\t", na.strings = "null", shiny=shiny, message=message)
 }

Which in turn runs:

if(is.null(colInt)){
  colInt <- MSnbase::grepEcols(file, pattern=pattern, split = sep)
  }
  peptides <- MSnbase::readMSnSet2(file, ecol = colInt, sep = sep, na.strings = na.strings, quote = quote, comment.char = comment.char, stringsAsFactors = TRUE, ...)

I've tried running this segment (adapted to run properly) of code to read in the mzTab file and I get the same empty MSnSet object, even when I change pattern to "peptide_abundance_assay".

However, if I run:

peptides<-readMzTabData("path_to_mzTab", "PEP")
> head(exprs(pepMat))
                 peptide_abundance_assay.1. peptide_abundance_assay.2. peptide_abundance_assay.3. peptide_abundance_assay.4. peptide_abundance_assay.5. peptide_abundance_assay.6.
NKLEGLEDALQK                        2656000                    5639000                    2768000                    7279000                    2619000                    1646000
NKLEGLEDALQK.1                      2656000                    5639000                    2768000                    7279000                    2619000                    1646000
NKLEGLEDALQK.2                      2656000                    5639000                    2768000                    7279000                    2619000                    1646000
NKLEGLEDALQK.3                      2656000                    5639000                    2768000                    7279000                    2619000                    1646000
LQDAEEAVEAVNAK                           NA                         NA                         NA                         NA                         NA                         NA
LQDAEEAVEAVNAK.1                         NA                         NA                         NA

It appears to work and creates MSnSet object with peptide intensities. I'm now following the rest of the example workflow to see if I can get it to work.

Regards,

Craig
@ludgergoeminne
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Dear cdlawless

Most of the import files which I have tested when developing MSqRob came from MaxQuant input.
Other file formats were added on requests of users who were willing to share (part of) their data.
The readMzTabData function works for the files which I have, but it is possible that there might be some issue with reading in your files.
If you would be willing to share a small example file, I could check where the exact problem is.
Once the data is imported as an MSnSet object, the workflow is independent of the input format.

Best regards

Ludger

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@cdlawless @ludgergoeminne
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