On data outputs

You can access the enviMass R screening results in the following way:
    Results for the target/suspect and internal standard (ISTD) screening can be found in the results/screening folder of your enviMass project. In the following, this is outlined for target screening results. The same applies to ISTD screening results by adapting the R object file names accordingly (shown partly in brackets below).

    The screening results are saved as three-level R lists by enviMass and can be loaded via:

    load(file.path(project_folder,"results","screening","res_target_pos_screen"))

    ("res_IS_pos_screen") and

    load(file.path(project_folder,"results","screening","res_target_neg_screen"))

    ("res_IS_neg_screen") for the positive and negative ionization modes, repectively. Note that project_folder must state a valid path to your enviMass project folder, containing a logfile.emp file. In summary, these three below outlined list levels are:

    • res_target_pos_screen[[X]]: screening results over X compounds and different adducts.
    • res_target_pos_screen[[X]][[Y]] : screening results over Y files for one compound and one of its adducts.
    • res_target_pos_screen[[X]][[Y]][[Z]] : different screening results for Z different peak combinations for one file and for one compound and one of its adducts.




    The first level in the loaded list states the individual screening results over the expansion of target compounds and their individual adducts, and can be accessed via the list names

    names(res_target_pos_screen)

    where each name consists of a ID_adduct_Remark_tag1_tag2 concatenation. All concatenation entries expect for adduct refer to columns in the → target compound table (ISTD) stored as targets (IS) in the dataframes folder of your project, which can be loaded via load(...) as well. Thus, each first-level list entry contains all the screening results for one compound and one of its adducts. This entry can (a) be empty if no screening matches where found for any of the used files or (b) contains itself another list of the length of the used files if at least one screening match was found for any of these files. For example,

    res_target_pos_screen[[1]] or
    res_target_pos_screen[["201_M+H_FALSE_none_none"]]

    gives you the IDs of files with screening matches for the first first-level entry in the list for compound with ID=201 and its M+H adduct. Again, file names are not given if no screening matches where aqcuired (= empty entry in the second-level list) or yet a third-level list with valid peak combinations for different screening matches. For example,

    res_target_pos_screen[[1]][[1]] or
    res_target_pos_screen[["201_M+H_FALSE_none_none"]][["5"]]

    lists all screening peak combinations for this first compound and the first screened file with file ID=5. In turn, file information such as file IDs or file names can be retrieved from The R measurements object also located in the dataframes folder of your project (can be loaded but must NOT be manipulated). This third and last list level can be accessed via, e.g.,

    res_target_pos_screen[[1]][[1]][[1]] or
    res_target_pos_screen[["201_M+H_FALSE_none_none"]][["5"]][[1]]

    and contains yet another list itself. Only one such list may be available if only one peak combination has lead to a screening result. Each such list contains another 10 entries, namely:

    names(res_target_pos_screen[[1]][[1]][[1]])

    which each detail:

    • res_target_pos_screen[[1]][[1]][[1]]$Peaks: The IDs of the indivual peak combination to match the theoretical centroided isotopologue pattern of the compound and its adduct.
    • $score_1: Matching score for peaks to be expected above the effective and rather conservative LOD.
    • $score_2: Additional matching score for peaks found below the effective LOD (optional).
    • $ppm deviation: Mass deviation of peaks from theoretical centroided isotopologue pattern.
    • $RT deviation from mean: Peak RT deviation from RT mean of all screened $Peaks.
    • $rescale factor: Ignore.
    • $m/z: Masses of the peaks.
    • $Intensity: Intensity of the peaks.
    • $RT: of peaks
    • $file_ID

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