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Export a mzTab-M 2.1 file

Source: R/export.R
MzTabM-export.Rd

Write and validate an mzTab-M (version 2.1) file.

The writer recognises the four standard sections:

  • MTD (Metadata): Always required. The metadata section provides additional information about the dataset(s) reported in the mzTab-M 2.1 file.

  • SML (Small Molecule Summary): Optional. Each row of the small molecule section is intended to report one final result to be communicated in terms of a molecule that has been quantified.

  • SMF (Small Molecule Feature): Optional but required when the SME section is present. The small molecule feature section represents individual MS regions that have been measured/quantified. Each SMF row SHOULD represent a single isotopomer.

  • SME (Small Molecule Evidence): Optional. The small molecule evidence section represents evidence for identifications of small molecules/features. In a typical case, each row represents one result from a single search or intepretation of a piece of evidence.

Column names of SMH, SFH and SEH are used as section headers.

Usage

writeMzTabM(x, path, comments = character(), validate = TRUE)

Arguments

x

list containing the mzTab-M data to be written.

path

character(1) with the path where save the mzTab-M file.

comments

character vector of comments to add to the file. The comments will be written after the MTD section and before any other section.

validate

logical(1) to run the validation on the exported file. Default: TRUE.

Value

The function does not return a value but, if the validation is performed, it writes the validation report.

Author

Gabriele Tomè

Examples


## Basic usage
exp <- data.frame(
    sample_name = c("S1_T1", "S1_T2", "S2_T1", "S2_T2", "S3_T1", "S3_T2"),
    sample_id = c("S1", "S1", "S2", "S2", "S3", "S3"),
    timepoint = c("0h", "6h", "0h", "6h", "0h", "6h"),
    genotype = c("WT", "WT", "KO", "KO", "KO", "KO"),
    operator = c("BB", "BB", "BB", "BB", "FB", "FB"),
    file_name = c("s1-t1.mzML", "s1-t2.mzML", "s2-t1.mzML", "s2-t2.mzML",
                 "s3-t1.mzML", "s3-t2.mzML")
)
mtd <- mtdSkeleton(id = "EXP_1", software = "[MS, MS:1001582, xcms, 4.1.0]")

mtd_s <- mtdSample(sample = unique(exp$sample_id))
mtd <- rbind(mtd, mtd_s)

mtd_msr <- mtdMsRun(
    location = exp$file_name,
    format = "[MS, MS:1000584, mzML file, ]",
    id_format = "[MS, MS:1000530, mzML unique identifier, ]",
    scan_polarity = "positive")
mtd <- rbind(mtd, mtd_msr)

mtd_a <- mtdAssay(
    assay = exp$sample_name,
    sample_ref = c("sample[1]", "sample[1]", "sample[2]", "sample[2]",
                   "sample[3]", "sample[3]"),
    ms_run_ref = paste0("ms_run[", seq_len(nrow(exp)), "]")
)
mtd <- rbind(mtd, mtd_a)

mtd_svar <- mtdStudyVariables(
    exp, groups = c("timepoint", "genotype", "operator"),
    group_unit = c("[, , hours, ]", "", ""))
mtd <- rbind(mtd, mtd_svar)
mtd <- mtdSort(mtd)

x <- list("MTD" = mtd)
filepath <- file.path(tempdir(), "example.mztab")

result <- writeMzTabM(x, path = filepath)
#> Validation finished successfully: 4 message(s) found, including:
#> 	- Info(s): 4
#> 	- Warning(s): 0
#> 	- Error(s): 0
#> 
#> Validation messages:
#>   level code line_no
#> 1  Info 2057      -1
#> 2  Info 2057      -1
#> 3  Info 2057      -1
#> 4  Info 2057      -1
#>                                                                                                                                                         text
#> 1 "quantification_method" is present but the profile "M" has no "small molecule summary (SML)/small molecule feature (SMF)" section that would require it.\r
#> 2                 "small_molecule-quantification_unit" is present but the profile "M" has no "small molecule summary (SML)" section that would require it.\r
#> 3         "small_molecule_feature-quantification_unit" is present but the profile "M" has no "small molecule feature (SMF)" section that would require it.\r
#> 4                                          "database" is present but the profile "M" has no "small molecule evidence (SME)" section that would require it.\r

## Add comments
comments <- c("Test comment")
results <- writeMzTabM(x, path = filepath, comments = comments)
#> Validation finished successfully: 4 message(s) found, including:
#> 	- Info(s): 4
#> 	- Warning(s): 0
#> 	- Error(s): 0
#> 
#> Validation messages:
#>   level code line_no
#> 1  Info 2057      -1
#> 2  Info 2057      -1
#> 3  Info 2057      -1
#> 4  Info 2057      -1
#>                                                                                                                                                         text
#> 1 "quantification_method" is present but the profile "M" has no "small molecule summary (SML)/small molecule feature (SMF)" section that would require it.\r
#> 2                 "small_molecule-quantification_unit" is present but the profile "M" has no "small molecule summary (SML)" section that would require it.\r
#> 3         "small_molecule_feature-quantification_unit" is present but the profile "M" has no "small molecule feature (SMF)" section that would require it.\r
#> 4                                          "database" is present but the profile "M" has no "small molecule evidence (SME)" section that would require it.\r

## Run without the validate
results <- writeMzTabM(x, path = filepath, validate = FALSE)