diff --git a/R/MzTabParam.R b/R/MzTabParam.R index 8563e440..0b80eafc 100644 --- a/R/MzTabParam.R +++ b/R/MzTabParam.R @@ -175,7 +175,7 @@ setMethod("storeResults", base[base == "replace_id"] <- study_id msrun <- cbind( name = paste0("ms_run[", seq_sample, "]-location"), - value = unlist(fileNames(object)), + value = paste0("file:///", unlist(gsub(" ", "",fileNames(object)))), order = .prefix_zero(seq_sample) ) if (polarity == "positive") { @@ -193,8 +193,8 @@ setMethod("storeResults", msrun <- msrun[order(msrun[, "order"]), c("name", "value")] assay <- cbind( - name = paste("assay", seq_sample), - value = paste0("assay[", seq_sample, "]"), + name = paste0("assay[", seq_sample, "]"), + value = paste(seq_sample, "assay"), order = .prefix_zero(seq_sample) ) assay_ref <- cbind( @@ -214,7 +214,9 @@ setMethod("storeResults", var, base[5:nrow(base), ] ) - cbind(id = "MTD", mtd) + mtd <- cbind(id = "MTD", mtd) + + gsub("\\\\", "/", mtd) } #' @description @@ -241,7 +243,7 @@ setMethod("storeResults", #' Create the small molecule feature (SMF) `matrix` One row is one feature #' defined in xcms. Use the .SMF static object. #' object as a basis. -#' +#'read #' @noRd #' #' @param object `XcmsExperiment`. @@ -343,8 +345,10 @@ setMethod("storeResults", res, matrix(ncol = 2, c(paste0("study_variable[", i, "]"), + paste0("study_variable[", i, "]-description"), paste0("study_variable[", i, "]-assay_refs"), paste0(unique_svar[i]), + paste0("Sample in column ", unique_svar[i]), #either this or paste0("assay[", idx[, "row"], "]", collapse = sep) ))) } @@ -363,6 +367,7 @@ setMethod("storeResults", } ### Static objects + .MTD <- cbind( name = c("mzTab-version", "mzTab-ID", @@ -372,28 +377,32 @@ setMethod("storeResults", "cv[1]-full_name", "cv[1]-version", "cv[1]-uri", + "cv[2]-label", + "cv[2]-full_name", + "cv[2]-version", + "cv[2]-uri", "database[1]", "database[1]-prefix", "database[1]-version", "database[1]-uri", - "small_molecule-quantification_unit", - "small_molecule_feature-quantification_unit", - "id_confidence_measure[1]"), + "small_molecule_feature-quantification_unit"), value = c("2.0.0-M", "replace_id", - "[MS, MS:4711, xcms, 3.1.1]", - "[MS, MS:1001834, LC-MS label-free quantitation analysis]", + "[MS, MS:1001582, XCMS, 3.1.1]", + "[MS, MS:1001834, LC-MS label-free quantitation analysis, ]", "MS", "PSI-MS controlled vocabulary", "4.1.138", "https://raw.githubusercontent.com/HUPO-PSI/psi-ms-CV/master/psi-ms.obo", + "PRIDE", + "PRIDE PRoteomics IDEntifications (PRIDE) database controlled vocabulary", + "16:10:2023 11:38", + "https://www.ebi.ac.uk/ols/ontologies/pride", "[,, \"no database\", null ]", "null", "Unknown", "null", - "null", - "[MS, MS:1001841, LC-MS feature volume, ]", - "null")) + "[PRIDE, PRIDE:0000330, Arbitrary quantification unit, ]")) .SML <- c("SMH", "SML_ID","SMF_ID_REFS", "database_identifier", "chemical_formula", "smiles", "inchi", "chemical_name", @@ -404,3 +413,4 @@ setMethod("storeResults", "adduct_ion", "isotopomer", "exp_mass_to_charge", "charge", "retention_time_in_seconds", "retention_time_in_seconds_start", "retention_time_in_seconds_end") +