wrProteo (version 1.13.1)

exportSdrfDraft: Export Sample Meta-data from Quantification-Software as Sdrf-draft

Description

Sample/experimental annotation meta-data form MaxQuant that was previously import can now be formatted in sdrf-style and exported using this function to write a draft-sdrf-file. Please note that this information will not _complete_ in respect to all information used in data-bases like Pride. Sdrf-files provide additional meta-information about samles and MS-runs in a standardized format, they may also be part of submissions to Pride.

Usage

exportSdrfDraft(
  lst,
  fileName = "sdrfDraft.tsv",
  correctFileExtension = TRUE,
  silent = FALSE,
  debug = FALSE,
  callFrom = NULL
)

Value

This function writes an Sdrf draft to file

Arguments

lst

(list) object created by import-function (MaxQuant)

fileName

(character) file-name (and path) to be used when exprting

correctFileExtension

(logical) if TRUE the fileName will get a .tsv-extension if not already present

silent

(logical) suppress messages

debug

(logical) additional messages for debugging

callFrom

(character) allow easier tracking of messages produced

Details

Gathering as much as possible information about samples and MS-runs requires that the additional files created from software, like MaxQuant using readMaxQuantFile, is present and was imported when calling the import-function (eg using the argument _suplAnnotFile=TRUE_). Please note that this functionality was designed for the case where no (external) sdrf-file is available. Thus, when data was imported including exteranl sdrf (uinsg the _sdrf=_ argument), exporting incomplete annotation-data from MaxQuant-produced files does not make any sense and therefore won't be possible.

After exporting the draft sdrf the user is advised to check and complete the information in the resulting file. Unfortunately, not all information present in a standard sdrf-file (like on Pride) cannot be gathered automatically, but key columns are already present and thus may facilitate completing. Please note, that the file-format has been defined as .tsv, thus columns/fields should be separated by tabs. At manual editing and completion, some editing- or tabulator-software may change the file-extesion to .tsv.txt, in this case the final files should be renamed as .tsv to remain compatible with Pride.

At this point only the import of data from MaxQuant via readMaxQuantFile has been developed to extract information for creating a draft-sdrf. Other data/file-import functions may be further developed to gather as much as possible equivalent information in the future.

See Also

This function may be used after reading/importig data by readMaxQuantFile in absence of sdrf

Examples

path1 <- system.file("extdata", package="wrProteo")
fiNaMQ <- "proteinGroups.txt.gz"
dataMQ <- readMaxQuantFile(path1, file=fiNaMQ, refLi="mainSpe", sdrf=FALSE, suplAnnotFile=TRUE)
## Here we'll write simply in the current temporary directory of this R-session
exportSdrfDraft(dataMQ, file.path(tempdir(),"testSdrf.tsv"))