{ "_id": "6a1abe221d7bb097a09d6315", "Package": "RAIDS", "Type": "Package", "Title": "Robust Ancestry Inference using Data Synthesis", "Description": "This package implements specialized algorithms that enable\ngenetic ancestry inference from various cancer sequences\nsources (RNA, Exome and Whole-Genome sequences). This package\nalso implements a simulation algorithm that generates synthetic\ncancer-derived data. This code and analysis pipeline was\ndesigned and developed for the following publication: Belleau,\nP et al. Genetic Ancestry Inference from Cancer-Derived\nMolecular Data across Genomic and Transcriptomic Platforms.\nCancer Res 1 January 2023; 83 (1): 49–58.", "Version": "1.11.0", "Authors@R": "c(person(\"Pascal\", \"Belleau\", email=\"pascal_belleau@hotmail.com\",\nrole=c(\"cre\", \"aut\"), comment = c(ORCID = \"0000-0002-0802-1071\")),\nperson(\"Astrid\", \"Deschênes\", email=\"adeschen@hotmail.com\",\nrole=c(\"aut\"), comment = c(ORCID = \"0000-0001-7846-6749\")),\nperson(given=\"David A.\", family=\"Tuveson\",\nemail=\"dtuveson@cshl.edu\",\nrole=c(\"aut\"), comment=c(ORCID=\"0000-0002-8017-2712\")),\nperson(\"Alexander\", \"Krasnitz\", email=\"krasnitz@cshl.edu\",\nrole=c(\"aut\")))", "License": "Apache License (>= 2)", "Encoding": "UTF-8", "NeedsCompilation": "no", "VignetteBuilder": "knitr", "BugReports": "https://github.com/KrasnitzLab/RAIDS/issues", "URL": "https://krasnitzlab.github.io/RAIDS/", "biocViews": "Genetics, Software, Sequencing, WholeGenome,\nPrincipalComponent, GeneticVariability, DimensionReduction,\nBiocViews", "Roxygen": "list(markdown = TRUE)", "RoxygenNote": "7.3.2", "Config/pak/sysreqs": "cmake libglpk-dev make libbz2-dev libicu-dev\nliblzma-dev libpng-dev libxml2-dev libssl-dev libx11-dev\nxz-utils zlib1g-dev", "Repository": "https://bioc.r-universe.dev", "Date/Publication": "2026-04-28 13:01:38 UTC", "RemoteUrl": "https://github.com/bioc/RAIDS", "RemoteRef": "HEAD", "RemoteSha": "40c776e9ab01ca0cd7224b5665739523fce68820", "Packaged": { "Date": "2026-05-30 07:10:37 UTC", "User": "root" }, "Author": "Pascal Belleau [cre, aut] (ORCID:\n),\nAstrid Deschênes [aut] (ORCID: ),\nDavid A. Tuveson [aut] (ORCID: ),\nAlexander Krasnitz [aut]", "Maintainer": "Pascal Belleau ", "MD5sum": "f64e60ecfe281626a33211a86dddb727", "_user": "bioc", "_type": "src", "_file": "RAIDS_1.11.0.tar.gz", "_fileid": "627f90c883edd2b91fbf7f1d17943d9e06577da6c496be74094e4789549f86c6", "_filesize": 3263113, "_sha256": "627f90c883edd2b91fbf7f1d17943d9e06577da6c496be74094e4789549f86c6", "_created": "2026-05-30T07:10:37.000Z", "_published": "2026-05-30T10:38:26.869Z", "_jobs": [ { "job": 78632627238, "time": 339, "config": "bioc-checks", "r": "4.6.0", "check": "NOTE", "artifact": "7306394858" }, { "job": 78632627223, "time": 612, "config": "linux-devel-x86_64", "r": "4.7.0", "check": "NOTE", "artifact": "7306425891" }, { "job": 78632627217, "time": 600, "config": "linux-release-x86_64", "r": "4.6.0", "check": "NOTE", "artifact": "7306424614" }, { "job": 78632627244, "time": 386, "config": "macos-oldrel-arm64", "r": "4.5.3", "check": "NOTE", "artifact": "7307335283" }, { "job": 78632627224, "time": 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Beware that the PCA has been run on a very small subset of the 1KG reference dataset and should not be used to call ancestry inference on a real profile.", "topics": [ "demoPCA1KG" ] }, { "page": "demoPCASyntheticProfiles", "title": "The PCA result of demo synthetic profiles projected on the demo subset 1KG reference PCA.", "topics": [ "demoPCASyntheticProfiles" ] }, { "page": "demoPedigreeEx1", "title": "The pedigree information about a demo profile called 'ex1'.", "topics": [ "demoPedigreeEx1" ] }, { "page": "estimateAllelicFraction", "title": "Estimate the allelic fraction of the pruned SNVs for a specific profile", "topics": [ "estimateAllelicFraction" ] }, { "page": "generateGDS1KG", "title": "Generate the GDS file that will contain the information from Reference data set (reference data set)", "topics": [ "generateGDS1KG" ] }, { "page": "generateMapSnvSel", "title": "Generate the filter SNP information file in RDS format", "topics": [ "generateMapSnvSel" ] }, { "page": "generatePhase1KG2GDS", "title": "Adding the phase information into the Reference GDS file", "topics": [ "generatePhase1KG2GDS" ] }, { "page": "generatePhaseRef", "title": "Adding the phase information into the Reference GDS file", "topics": [ "generatePhaseRef" ] }, { "page": "getRef1KGPop", "title": "Extract the specified column from the 1KG GDS 'sample.ref' node for the reference profiles (real ancestry assignation)", "topics": [ "getRef1KGPop" ] }, { "page": "getRefSuperPop", "title": "Extract the from the 1KG GDS 'sample.ref' node for the reference profiles (real ancestry assignation)", "topics": [ "getRefSuperPop" ] }, { "page": "groupChr1KGSNV", "title": "Merge the genotyping files per chromosome into one file", "topics": [ "groupChr1KGSNV" ] }, { "page": "identifyRelative", "title": "Identify genetically unrelated patients in GDS Reference file", "topics": [ "identifyRelative" ] }, { "page": "identifyRelativeRef", "title": "Identify genetically unrelated patients in GDS Reference file", "topics": [ "identifyRelativeRef" ] }, { "page": "inferAncestry", "title": "Run most steps leading to the ancestry inference call on a specific DNA profile", "topics": [ "inferAncestry" ] }, { "page": "inferAncestryDNA", "title": "Run most steps leading to the ancestry inference call on a specific DNA profile (alias for inferAncestry )", "topics": [ "inferAncestryDNA" ] }, { "page": "inferAncestryGeneAware", "title": "Run most steps leading to the ancestry inference call on a specific RNA profile", "topics": [ "inferAncestryGeneAware" ] }, { "page": "matKNNSynthetic", "title": "A small 'data.frame' containing the inferred ancestry on the synthetic profiles.", "topics": [ "matKNNSynthetic" ] }, { "page": "pedSynthetic", "title": "A small 'data.frame' containing the information related to synthetic profiles. The ancestry of the profiles used to generate the synthetic profiles must be present.", "topics": [ "pedSynthetic" ] }, { "page": "prepPed1KG", "title": "Prepare the pedigree file using pedigree information from Reference", "topics": [ "prepPed1KG" ] }, { "page": "prepSynthetic", "title": "Add information related to the synthetic profiles (study and synthetic reference profiles information) into a Profile GDS file", "topics": [ "prepSynthetic" ] }, { "page": "pruningSample", "title": "Compute the list of pruned SNVs for a specific profile using the information from the Reference GDS file and a linkage disequilibrium analysis", "topics": [ "pruningSample" ] }, { "page": "runExomeAncestry", "title": "Run most steps leading to the ancestry inference call on a specific exome profile", "topics": [ "runExomeAncestry" ] }, { "page": "runRNAAncestry", "title": "Run most steps leading to the ancestry inference call on a specific RNA profile", "topics": [ "runRNAAncestry" ] }, { "page": "select1KGPop", "title": "Random selection of a specific number of reference profiles in each subcontinental population present in the 1KG GDS file", "topics": [ "select1KGPop" ] }, { "page": "select1KGPopForSynthetic", "title": "Random selection of a specific number of reference profiles in each subcontinental population present in the 1KG GDS file ( same as select1KGPop but the function doesn't need gds object as parameters but the file name of the referenceGDS )", "topics": [ "select1KGPopForSynthetic" ] }, { "page": "snpPositionDemo", "title": "A small 'data.frame' containing the SNV information.", "topics": [ "snpPositionDemo" ] }, { "page": "snvListVCF", "title": "Generate a VCF with the information from the SNPs that pass a cut-off threshold", "topics": [ "snvListVCF" ] }, { "page": "splitSelectByPop", "title": "Group samples per subcontinental population", "topics": [ "splitSelectByPop" ] }, { "page": "syntheticGeno", "title": "Generate synthetic profiles for each cancer profile and 1KG reference profile combination and add them to the Profile GDS file", "topics": [ "syntheticGeno" ] } ], "_readme": "https://github.com/bioc/RAIDS/raw/HEAD/README.md", "_rundeps": [ "abind", "AnnotationDbi", "AnnotationFilter", "askpass", "backports", "BH", "Biobase", "BiocBaseUtils", "BiocGenerics", "BiocIO", "BiocParallel", "Biostrings", "bit", "bit64", "bitops", "blob", "boot", "broom", "BSgenome", "cachem", "cigarillo", "class", "cli", "clipr", "codetools", "cpp11", "crayon", "curl", "data.table", "DBI", "DelayedArray", "digest", "DNAcopy", "dplyr", "ensembldb", "farver", "fastmap", "forcats", "foreach", "formatR", "formula.tools", "futile.logger", "futile.options", "gdsfmt", "generics", "GENESIS", "GenomeInfoDb", "GenomicAlignments", "GenomicFeatures", "GenomicRanges", "ggplot2", "glmnet", "glue", "gtable", "GWASExactHW", "GWASTools", "haven", "hms", "httr", "igraph", "IRanges", "isoband", "iterators", "jomo", "jsonlite", "KEGGREST", "labeling", "lambda.r", "lattice", "lazyeval", "lifecycle", "lme4", "lmtest", "logistf", "magrittr", "MASS", "Matrix", "MatrixGenerics", "MatrixModels", "matrixStats", "memoise", "mgcv", "mice", "mime", "minqa", "mitml", "nlme", "nloptr", "nnet", "numDeriv", "openssl", "operator.tools", "ordinal", "pan", "pillar", "pkgconfig", "plyr", "png", "prettyunits", "pROC", "progress", "ProtGenerics", "purrr", "quantreg", "quantsmooth", "R6", "rbibutils", "RColorBrewer", "Rcpp", "RcppEigen", "RCurl", "Rdpack", "readr", "reformulas", "reshape2", "restfulr", "RhpcBLASctl", "Rhtslib", "rjson", "rlang", "rpart", "Rsamtools", "RSQLite", "rtracklayer", "S4Arrays", "S4Vectors", "S7", "sandwich", "scales", "SeqArray", "Seqinfo", "SeqVarTools", "shape", "snow", "SNPRelate", "SparseArray", "SparseM", "stringi", "stringr", "SummarizedExperiment", "survival", "sys", "tibble", "tidyr", "tidyselect", "tzdb", "ucminf", "UCSC.utils", "utf8", "VariantAnnotation", "vctrs", "viridisLite", "vroom", "withr", "XML", "XVector", "yaml", "zoo" ], "_vignettes": [ { "source": "Create_Reference_GDS_File.Rmd", "filename": "Create_Reference_GDS_File.html", "title": "Population reference dataset GDS files", "author": "Pascal Belleau, Astrid Deschênes and Alexander Krasnitz", "engine": "knitr::rmarkdown", "headings": [ "Population Reference GDS File", "Population Reference Annotation GDS file", "Pre-processed files, from 1000 Genomes in hg38, are available", "Session info", "References" ], "created": "2023-08-14 05:57:36", "modified": "2023-09-29 21:21:15", "commits": 18 }, { "source": "RAIDS.Rmd", "filename": "RAIDS.html", "title": "Robust Ancestry Inference using Data Synthesis", "author": "Pascal Belleau, Astrid Deschênes and Alexander Krasnitz", "engine": "knitr::rmarkdown", "headings": [ "Licensing", "Citing", "Introduction", "Installation", "Using RAIDS: step-by-step explanation", "Step 1. 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