Adeschen patch 1

.github/workflows/check-bioc.yaml

@@ -51,10 +51,11 @@ jobs:
       fail-fast: false
       matrix:
         config:
-          -  { os: ubuntu-latest, r: '4.2.2', bioc: '3.16', cont: "bioconductor/bioconductor_docker:RELEASE_3_16", rspm: "https://packagemanager.posit.co" }
-        ##  - { os: ubuntu-latest, r: '4.3', bioc: '3.17', cont: "bioconductor/bioconductor_docker:RELEASE_3_17", rspm: "https://packagemanager.posit.co/cran/__linux__/jammy/latest" }
-          - { os: macOS-latest, r: '4.2.2', bioc: '3.16'}
-         ## - { os: windows-latest, r: '4.2.2', bioc: '3.16'}
+         - { os: ubuntu-latest, r: 'devel', bioc: '3.22', cont: "bioconductor/bioconductor_docker:RELEASE_3_22", rspm: "https://packagemanager.posit.co/cran/__linux__/jammy/latest" }
+         - { os: ubuntu-latest, r: '4.5.1', bioc: '3.21'}
+         - { os: macOS-latest, r: '4.5.1', bioc: '3.21'}
+         - { os: windows-latest, r: '4.5.1', bioc: '3.21'}
+
     env:
       R_REMOTES_NO_ERRORS_FROM_WARNINGS: true
       RSPM: ${{ matrix.config.rspm }}
@@ -77,7 +78,7 @@ jobs:
       ## https://github.com/r-lib/actions/blob/master/examples/check-standard.yaml
       ## If they update their steps, we will also need to update ours.
       - name: Checkout Repository
-        uses: actions/checkout@v3
+        uses: actions/checkout@v4
 
       ## R is already included in the Bioconductor docker images
       - name: Setup R from r-lib
@@ -100,15 +101,15 @@ jobs:
 
       - name: Cache R packages
         if: "!contains(github.event.head_commit.message, '/nocache') && runner.os != 'Linux'"
-        uses: actions/cache@v3
+        uses: actions/cache@v4
         with:
           path: ${{ env.R_LIBS_USER }}
           key: ${{ env.cache-version }}-${{ runner.os }}-biocversion-RELEASE_$${{ matrix.config.bioc }}-$${{ matrix.config.r }}-${{ hashFiles('.github/depends.Rds') }}
           restore-keys: ${{ env.cache-version }}-${{ runner.os }}-biocversion-RELEASE_$${{ matrix.config.bioc }}-r-${{ matrix.config.r }}-
 
       - name: Cache R packages on Linux
         if: "!contains(github.event.head_commit.message, '/nocache') && runner.os == 'Linux' "
-        uses: actions/cache@v3
+        uses: actions/cache@v4
         with:
           path: /home/runner/work/_temp/Library
           key: ${{ env.cache-version }}-${{ runner.os }}-biocversion-RELEASE_$${{ matrix.config.bioc }}-r-${{ matrix.config.r }}--${{ hashFiles('.github/depends.Rds') }}

.github/workflows/test-coverage.yaml

@@ -2,9 +2,7 @@
 # Need help debugging build failures? Start at https://github.com/r-lib/actions#where-to-find-help
 on:
   push:
-    branches: main
   pull_request:
-    branches: main
 
 name: test-coverage
 
@@ -15,7 +13,7 @@ jobs:
       GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
 
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
 
       - uses: r-lib/actions/setup-r@v2
         with:
@@ -29,3 +27,5 @@ jobs:
       - name: Test coverage
         run: covr::codecov(quiet = FALSE)
         shell: Rscript {0}
+        env:
+          CODECOV_TOKEN: ${{ secrets.CODECOV_TOKEN }}

DESCRIPTION

@@ -1,6 +1,6 @@
 Package: RAIDS
 Type: Package
-Title: Accurate Inference of Genetic Ancestry from Cancer Sequences
+Title: Robust Ancestry Inference using Data Synthesis
 Description: This package implements specialized algorithms that enable
     genetic ancestry inference from various cancer sequences sources (RNA,
     Exome and Whole-Genome sequences). This package also implements a
@@ -9,11 +9,14 @@ Description: This package implements specialized algorithms that enable
     following publication: Belleau, P et al. Genetic Ancestry Inference from 
     Cancer-Derived Molecular Data across Genomic and Transcriptomic 
     Platforms. Cancer Res 1 January 2023; 83 (1): 49–58.
-Version: 0.99.4
+Version: 1.7.1
 Authors@R: c(person("Pascal", "Belleau", email="pascal_belleau@hotmail.com",
     role=c("cre", "aut"), comment = c(ORCID = "0000-0002-0802-1071")),
     person("Astrid", "Deschênes", email="adeschen@hotmail.com",
     role=c("aut"), comment = c(ORCID = "0000-0001-7846-6749")),
+    person(given="David A.", family="Tuveson",
+    email="dtuveson@cshl.edu", 
+    role=c("aut"), comment=c(ORCID="0000-0002-8017-2712")),
     person("Alexander", "Krasnitz", email="krasnitz@cshl.edu",
     role=c("aut")))
 License: Apache License (>= 2)
@@ -25,7 +28,9 @@ Depends: R (>= 4.2.0),
     SNPRelate,
     stats,
     utils,
-    GENESIS
+    GENESIS,
+    dplyr,
+    Rsamtools
 Imports: S4Vectors,
     GenomicRanges,
     ensembldb,
@@ -36,15 +41,22 @@ Imports: S4Vectors,
     pROC,
     IRanges,
     AnnotationFilter,
-    rlang
+    rlang,
+    VariantAnnotation,
+    MatrixGenerics,
+    ggplot2,
+    stringr
 Suggests: testthat,
     knitr,
     rmarkdown,
     BiocStyle,
     withr,
-    BSgenome.Hsapiens.UCSC.hg38
+    GenomeInfoDb,
+    BSgenome.Hsapiens.UCSC.hg38,
+    EnsDb.Hsapiens.v86
 BugReports: https://github.com/KrasnitzLab/RAIDS/issues
 URL: https://krasnitzlab.github.io/RAIDS/
 biocViews: Genetics, Software, Sequencing, WholeGenome, PrincipalComponent, 
-    GeneticVariability, DimensionReduction
-RoxygenNote: 7.2.3
+    GeneticVariability, DimensionReduction, BiocViews
+Roxygen: list(markdown = TRUE)
+RoxygenNote: 7.3.2

NAMESPACE

@@ -1,37 +1,42 @@
 # Generated by roxygen2: do not edit by hand
 
 export(add1KG2SampleGDS)
-export(addBlockFromPlink2GDS)
+export(addBlockFromDetFile)
 export(addGeneBlockGDSRefAnnot)
-export(addPhase1KG2SampleGDSFromFile)
-export(addPhase1KG2SampleGDSFromGDS)
+export(addGeneBlockRefAnnot)
 export(addRef2GDS1KG)
 export(addStudy1Kg)
-export(appendStudy2GDS1KG)
-export(basePCASample)
+export(computeAncestryFromSynthetic)
 export(computeAncestryFromSyntheticFile)
 export(computeKNNRefSample)
 export(computeKNNRefSynthetic)
 export(computePCAMultiSynthetic)
 export(computePCARefSample)
-export(computePoolSyntheticAncestry)
 export(computePoolSyntheticAncestryGr)
-export(computePrunedPCARef)
 export(computeSyntheticROC)
+export(createAUROCGraph)
+export(createAccuracyGraph)
 export(createStudy2GDS1KG)
 export(estimateAllelicFraction)
 export(generateGDS1KG)
 export(generateMapSnvSel)
 export(generatePhase1KG2GDS)
+export(generatePhaseRef)
 export(getRef1KGPop)
+export(getRefSuperPop)
 export(groupChr1KGSNV)
 export(identifyRelative)
+export(identifyRelativeRef)
+export(inferAncestry)
+export(inferAncestryDNA)
+export(inferAncestryGeneAware)
 export(prepPed1KG)
 export(prepSynthetic)
-export(projectSample2PCA)
 export(pruningSample)
 export(runExomeAncestry)
+export(runRNAAncestry)
 export(select1KGPop)
+export(select1KGPopForSynthetic)
 export(snvListVCF)
 export(splitSelectByPop)
 export(syntheticGeno)
@@ -41,7 +46,15 @@ importFrom(BSgenome,strand)
 importFrom(GENESIS,pcairPartition)
 importFrom(GenomicRanges,GRanges)
 importFrom(GenomicRanges,reduce)
+importFrom(GenomicRanges,seqnames)
+importFrom(GenomicRanges,start)
+importFrom(GenomicRanges,width)
 importFrom(IRanges,IRanges)
+importFrom(MatrixGenerics,rowRanges)
+importFrom(Rsamtools,BamFile)
+importFrom(Rsamtools,PileupParam)
+importFrom(Rsamtools,ScanBamParam)
+importFrom(Rsamtools,pileup)
 importFrom(S4Vectors,Rle)
 importFrom(S4Vectors,aggregate)
 importFrom(S4Vectors,isSingleNumber)
@@ -52,7 +65,12 @@ importFrom(SNPRelate,snpgdsOpen)
 importFrom(SNPRelate,snpgdsPCA)
 importFrom(SNPRelate,snpgdsPCASNPLoading)
 importFrom(SNPRelate,snpgdsPCASampLoading)
+importFrom(VariantAnnotation,geno)
+importFrom(VariantAnnotation,readVcf)
 importFrom(class,knn)
+importFrom(dplyr,"%>%")
+importFrom(dplyr,group_by)
+importFrom(dplyr,summarize)
 importFrom(ensembldb,exonsBy)
 importFrom(ensembldb,genes)
 importFrom(ensembldb,toSAF)
@@ -71,9 +89,23 @@ importFrom(gdsfmt,read.gdsn)
 importFrom(gdsfmt,readmode.gdsn)
 importFrom(gdsfmt,sync.gds)
 importFrom(gdsfmt,write.gdsn)
+importFrom(ggplot2,aes)
+importFrom(ggplot2,element_rect)
+importFrom(ggplot2,element_text)
+importFrom(ggplot2,facet_grid)
+importFrom(ggplot2,geom_line)
+importFrom(ggplot2,geom_ribbon)
+importFrom(ggplot2,ggplot)
+importFrom(ggplot2,ggtitle)
+importFrom(ggplot2,scale_colour_manual)
+importFrom(ggplot2,theme)
+importFrom(ggplot2,theme_classic)
+importFrom(ggplot2,ylab)
+importFrom(ggplot2,ylim)
 importFrom(methods,is)
 importFrom(pROC,multiclass.roc)
 importFrom(pROC,roc)
+importFrom(rlang,.data)
 importFrom(rlang,arg_match)
 importFrom(stats,dbinom)
 importFrom(stats,mad)
@@ -82,6 +114,7 @@ importFrom(stats,pbinom)
 importFrom(stats,qbinom)
 importFrom(stats,quantile)
 importFrom(stats,rmultinom)
+importFrom(stringr,str_detect)
 importFrom(utils,read.csv)
 importFrom(utils,read.csv2)
 importFrom(utils,read.delim)