{ "_id": "6a196b32acfb0bcc41de9d61", "Package": "AWAggregator", "Type": "Package", "Title": "Attribute-Weighted Aggregation", "Version": "1.3.0", "Authors@R": "c(\nperson(given = \"Jiahua\",\nfamily = \"Tan\",\nemail = \"jiahuatan@chem.ubc.ca\",\nrole = c(\"aut\", \"cre\"),\ncomment = c(ORCID = \"0000-0001-5839-1049\")\n),\nperson(given = \"Gian L.\",\nfamily = \"Negri\",\nemail = \"gnegri@bcgsc.ca\",\nrole = c(\"aut\"),\ncomment = c(ORCID = \"0000-0001-7722-8888\")\n),\nperson(given = \"Gregg B.\",\nfamily = \"Morin\",\nemail = \"gmorin@bcgsc.ca\",\nrole = c(\"aut\"),\ncomment = c(ORCID = \"0000-0001-8949-4374\")\n),\nperson(given = \"David D. Y.\",\nfamily = \"Chen\",\nemail = \"chen@chem.ubc.ca\",\nrole = c(\"aut\"),\ncomment = c(ORCID = \"0000-0002-3669-6041\")\n)\n)", "Description": "This package implements an attribute-weighted aggregation\nalgorithm which leverages peptide-spectrum match (PSM)\nattributes to provide a more accurate estimate of protein\nabundance compared to conventional aggregation methods. This\nalgorithm employs pre-trained random forest models to predict\nthe quantitative inaccuracy of PSMs based on their attributes.\nPSMs are then aggregated to the protein level using a weighted\naverage, taking the predicted inaccuracy into account.\nAdditionally, the package allows users to construct their own\ntraining sets that are more relevant to their specific\nexperimental conditions if desired.", "License": "MIT + file LICENSE", "Encoding": "UTF-8", "Roxygen": "list(markdown = TRUE)", "RoxygenNote": "7.3.2", "biocViews": "Software, MassSpectrometry, Preprocessing, Proteomics,\nRegression", "BugReports": "https://github.com/Tan-Jiahua/AWAggregator/issues", "URL": "https://github.com/Tan-Jiahua/AWAggregator", "VignetteBuilder": "knitr", "Config/testthat/edition": "3", "Config/pak/sysreqs": "libicu-dev libssl-dev", "Repository": "https://bioc.r-universe.dev", "Date/Publication": "2026-04-28 13:05:17 UTC", "RemoteUrl": "https://github.com/bioc/AWAggregator", "RemoteRef": "HEAD", "RemoteSha": "a4529421f0e95302688ac14c33e20342ab327317", "NeedsCompilation": "no", "Packaged": { "Date": "2026-05-29 08:38:54 UTC", "User": "root" }, "Author": "Jiahua Tan [aut, cre] (ORCID: ),\nGian L. Negri [aut] (ORCID: ),\nGregg B. Morin [aut] (ORCID: ),\nDavid D. Y. Chen [aut] (ORCID: )", "Maintainer": "Jiahua Tan ", "MD5sum": "58923c3c49b73d3a4d2199cb324d99b4", "_user": "bioc", "_type": "src", "_file": "AWAggregator_1.3.0.tar.gz", "_fileid": "456eabbecacba92f6348b8ee2cd75720ba27832e249c3eb3b67d5d6c24290345", "_filesize": 185583, "_sha256": "456eabbecacba92f6348b8ee2cd75720ba27832e249c3eb3b67d5d6c24290345", "_created": "2026-05-29T08:38:54.000Z", "_published": "2026-05-29T10:32:18.063Z", "_jobs": [ { "job": 78467112090, "time": 172, "config": "bioc-checks", "r": "4.6.0", "check": "WARNING", "artifact": "7286663253" }, { "job": 78467112120, "time": 643, "config": "linux-devel-x86_64", "r": "4.7.0", "check": "OK", "artifact": "7286804584" }, { "job": 78467112060, "time": 316, "config": "linux-release-x86_64", "r": "4.6.0", "check": "OK", "artifact": "7286706741" }, { "job": 78467112056, "time": 285, "config": "macos-oldrel-arm64", "r": "4.5.3", "check": "OK", "artifact": "7288634500" }, { "job": 78467112047, "time": 285, "config": "macos-release-arm64", "r": "4.6.0", "check": "OK", "artifact": "7288634898" }, { "job": 78466248770, "time": 357, "config": "source", "r": "4.6.0", "check": "OK", "artifact": "7286613137" }, { "job": 78467112101, "time": 125, "config": "wasm-release", "r": "4.6.0", "check": "OK", "artifact": "7286649650" }, { "job": 78467112081, "time": 274, "config": "windows-devel", "r": "4.7.0", "check": "OK", "artifact": "7286693853" }, { "job": 78467112135, "time": 403, "config": "windows-oldrel", "r": "4.5.3", "check": "OK", "artifact": "7286732033" }, { "job": 78467112103, "time": 415, "config": "windows-release", "r": "4.6.0", "check": "OK", "artifact": "7286735974" } ], "_bioccheck": { "error": 0, "warning": 1, "note": 5 }, "_buildurl": "https://github.com/r-universe/bioc/actions/runs/26627029392", "_status": "success", "_host": "GitHub-Actions", "_upstream": "https://github.com/bioc/AWAggregator", "_commit": { "id": "a4529421f0e95302688ac14c33e20342ab327317", "author": "A Wokaty ", "committer": "A Wokaty ", "message": "bump x.y.z version to odd y following creation of RELEASE_3_23 branch\n", "time": 1777381517 }, "_maintainer": { "name": "Jiahua Tan", "email": "jiahuatan@chem.ubc.ca", "login": "tan-jiahua", "description": "", "uuid": 83559742, "orcid": "0000-0001-5839-1049" }, "_distro": "noble", "_registered": true, "_dependencies": [ { "package": "R", "version": ">= 4.5.0", "role": "Depends" }, { "package": "dplyr", "role": "Imports" }, { "package": "Peptides", "role": "Imports" }, { "package": "progress", "role": "Imports" }, { "package": "purrr", "role": "Imports" }, { "package": "ranger", "role": "Imports" }, { "package": "rlang", "role": "Imports" }, { "package": "stats", "role": "Imports" }, { "package": "stringr", "role": "Imports" }, { "package": "tidyr", "role": "Imports" }, { "package": "toOrdinal", "role": "Imports" }, { "package": "utils", "role": "Imports" }, { "package": "AWAggregatorData", "role": "Suggests" }, { "package": "BiocStyle", "role": "Suggests" }, { "package": "ExperimentHub", "role": "Suggests" }, { "package": "knitr", "role": "Suggests" }, { "package": "rmarkdown", "role": "Suggests" }, { "package": "testthat", "version": ">= 3.0.0", "role": "Suggests" } ], "_owner": "bioc", "_selfowned": true, "_usedby": 0, "_updates": [ { "week": "2025-33", "n": 1 }, { "week": "2025-34", "n": 1 }, { "week": "2025-44", "n": 2 }, { "week": "2026-18", "n": 2 } ], "_tags": [], "_bioc": [ { "branch": "devel", "version": "1.3.0", "bioc": "3.24" }, { "branch": "release", "version": "1.2.0", "bioc": "3.23" } ], "_topics": [ "software", "massspectrometry", "preprocessing", "proteomics", "regression" ], "_stars": 0, "_contributors": [ { "user": "tan-jiahua", "count": 4, "uuid": 83559742 } ], "_userbio": { "uuid": 2286807, "type": "organization", "name": "Bioconductor", "description": "Software for the analysis and comprehension of high-throughput genomic data" }, "_downloads": { "count": 182, "source": "https://www.bioconductor.org/packages/stats/bioc/AWAggregator" }, "_devurl": "https://github.com/tan-jiahua/awaggregator", "_searchresults": 4, "_rbuild": "4.6.0", "_assets": [ "extra/AWAggregator.html", "extra/citation.cff", "extra/citation.html", "extra/citation.json", "extra/citation.txt", "extra/contents.json", "extra/NEWS.html", "extra/NEWS.txt", "extra/readme.html", "extra/readme.md", "manual.pdf" ], "_homeurl": "https://github.com/tan-jiahua/awaggregator", "_realowner": "bioc", "_cranurl": false, "_exports": [ "aggregateByAttributes", "convertPDFormat", "fitQuantInaccuracyModel", "getAvgScaledErrorOfLog2FC", "getDistMetric", "getPSMAttributes", "mergeTrainingSets" ], "_datasets": [ { "name": "sample.prot.PD", "title": "Sample Protein Data from Protein Discoverer", "object": "sample.prot.PD", "file": "sample.prot.PD.rda", "class": [ "data.frame" ], "fields": [ "Accession", "Description" ], "rows": 5, "table": true, "tojson": true }, { "name": "sample.PSM.FP", "title": "Sample PSM Data from FragPipe", "object": "sample.PSM.FP", "file": "sample.PSM.FP.rda", "class": [ "data.frame" ], "fields": [ "Peptide", "Charge", "Calibrated Observed Mass", "Calibrated Observed M/Z", "Delta Mass", "Hyperscore", "Number of Missed Cleavages", "Intensity", "Assigned Modifications", "Purity", "Protein", "Sample 1", "Sample 2", "Sample 3", "Sample 4", "Sample 5", "Sample 6", "Sample 7", "Sample 8", "Sample 9" ], "rows": 118, "table": true, "tojson": true }, { "name": "sample.PSM.PD", "title": "Sample PSM Data from Proteome Discoverer", "object": "sample.PSM.PD", "file": "sample.PSM.PD.rda", "class": [ "data.frame" ], "fields": [ "Annotated Sequence", "Modifications", "Number of Proteins", "Master Protein Accessions", "Number of Missed Cleavages", "Charge", "mz in Da", "MHplus in Da", "Delta mz in Da", "Isolation Interference in Percent", "Average Reporter SN", "Sample 1", "Sample 2", "Sample 3", "Sample 4", "Sample 5", "Sample 6", "Sample 7", "Sample 8", "Sample 9", "XCorr" ], "rows": 128, "table": true, "tojson": true } ], "_help": [ { "page": "aggregateByAttributes", "title": "Aggregate PSMs to Protein Level", "topics": [ "aggregateByAttributes" ] }, { "page": "convertPDFormat", "title": "Convert Proteome Discoverer Output to Required Input Format", "topics": [ "convertPDFormat" ] }, { "page": "fitQuantInaccuracyModel", "title": "Fit a Random Forest Model", "topics": [ "fitQuantInaccuracyModel" ] }, { "page": "getAvgScaledErrorOfLog2FC", "title": "Get Average Scaled Error of log2FC for PSMs in a Spike-in Dataset", "topics": [ "getAvgScaledErrorOfLog2FC" ] }, { "page": "getDistMetric", "title": "Get Distance Metric", "topics": [ "getDistMetric" ] }, { "page": "getPSMAttributes", "title": "Get attributes for PSMs", "topics": [ "getPSMAttributes" ] }, { "page": "mergeTrainingSets", "title": "Merge Training Sets", "topics": [ "mergeTrainingSets" ] }, { "page": "sample.prot.PD", "title": "Sample Protein Data from Protein Discoverer", "topics": [ "sample.prot.PD" ] }, { "page": "sample.PSM.FP", "title": "Sample PSM Data from FragPipe", "topics": [ "sample.PSM.FP" ] }, { "page": "sample.PSM.PD", "title": "Sample PSM Data from Proteome Discoverer", "topics": [ "sample.PSM.PD" ] } ], "_readme": "https://github.com/bioc/AWAggregator/raw/HEAD/README.md", "_rundeps": [ "cli", "cpp11", "crayon", "curl", "dplyr", "generics", "glue", "hms", "jsonlite", "lattice", "lifecycle", "magrittr", "Matrix", "Peptides", "pillar", "pkgconfig", "pkgsearch", "prettyunits", "progress", "purrr", "R6", "ranger", "Rcpp", "RcppEigen", "rlang", "stringi", "stringr", "tibble", "tidyr", "tidyselect", "toOrdinal", "utf8", "vctrs", "withr" ], "_vignettes": [ { "source": "AWAggregator-vignette.Rmd", "filename": "AWAggregator-vignette.html", "title": "AWAggregator Vignette", "author": "Jiahua Tan, Gian L. Negri, Gregg B. Morin, David D. Y. Chen", "engine": "knitr::rmarkdown", "headings": [ "Introduction", "Overview of Package Functions", "Overview of Package Data", "Installation", "Workflow Examples", "Ex.1: Aggregate PSMs from FragPipe Using the Pre-Trained Model.", "Ex.2: Aggregate PSMs from Proteome Discoverer Using the Pre-Trained Model.", "Ex.3: Build a Merged Training Set and Retrain the Model.", "Step 1: Load Spike-in Datasets", "Step 2: Calculate PSM Attributes and Average Scaled Error of log~2~FC", "Step 3: Merge Spike-in Datasets as a New Training Set", "Step 4: Train a New Random Forest Model" ], "created": "2025-05-01 05:23:42", "modified": "2025-08-11 09:15:54", "commits": 2 } ], "_score": 4.301029995663981, "_indexed": true, "_nocasepkg": "awaggregator", "_universes": [ "bioc", "tan-jiahua" ], "_binaries": [ { "r": "4.7.0", "os": "linux", "version": "1.3.0", "date": "2026-05-29T08:42:39.000Z", "distro": "noble", "commit": "a4529421f0e95302688ac14c33e20342ab327317", "fileid": "9aff71c13194fb0c16618e54e68a1ecca143b7618706bcacb06ad5519b8a3552", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26627029392" }, { "r": "4.6.0", "os": "linux", "version": "1.3.0", "date": "2026-05-29T08:41:52.000Z", "distro": "noble", "commit": "a4529421f0e95302688ac14c33e20342ab327317", "fileid": "9c64ba6abd51c11015a0e3addb05e1f51be9299b2547b0cdc2d4a6e640f6c822", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26627029392" }, { "r": "4.5.3", "os": "mac", "version": "1.3.0", "date": "2026-05-29T10:28:19.000Z", "commit": "a4529421f0e95302688ac14c33e20342ab327317", "fileid": "029b51d881d49c19d554ce64c587aafaba8714c95f07b52709eaaa9818ab6e4a", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26627029392" }, { "r": "4.6.0", "os": "mac", "version": "1.3.0", "date": "2026-05-29T10:28:49.000Z", "commit": "a4529421f0e95302688ac14c33e20342ab327317", "fileid": "fc303aaa654c036e86425266b1aece5ee42b8a66805cc77f7ff14bdc1835ccd2", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26627029392" }, { "r": "4.6.0", "os": "wasm", "version": "1.3.0", "date": "2026-05-29T08:41:17.000Z", "commit": "a4529421f0e95302688ac14c33e20342ab327317", "fileid": "041484b43633bca7094d54280ba819b9076a536b406b8416c1aeca55a4537adc", "status": "success", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26627029392" }, { "r": "4.7.0", "os": "win", "version": "1.3.0", "date": "2026-05-29T08:40:28.000Z", "commit": "a4529421f0e95302688ac14c33e20342ab327317", "fileid": "7f45a09a9d0c7628180bcd96db39de319627619b1ef65816f861f4cefec35c89", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26627029392" }, { "r": "4.5.3", "os": "win", "version": "1.3.0", "date": "2026-05-29T08:40:24.000Z", "commit": "a4529421f0e95302688ac14c33e20342ab327317", "fileid": "39d3ed29099aeb52624303400c2a8426812e37d6f16ac44fadd686930de29a02", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26627029392" }, { "r": "4.6.0", "os": "win", "version": "1.3.0", "date": "2026-05-29T08:40:25.000Z", "commit": "a4529421f0e95302688ac14c33e20342ab327317", "fileid": "87ba25c619c822409c17ba285212422808cc5d74dff15b74097cef1dd4cd7a0c", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26627029392" } ] }