Using TCGAbiolinks to getTCGA data

.Rbuildignore

@@ -1,2 +1,9 @@
 ^.*\.Rproj$
 ^\.Rproj\.user$
+README.md
+ELMER.example.tar.xz
+^appveyor\.yml$
+^\.travis\.yml$
+^codecov\.yml$
+^doc$
+^Meta$

.gitattributes

@@ -0,0 +1,2 @@
+supplemental/ filter=lfs diff=lfs merge=lfs -text
+supplemental/BRCA_unsupervised.html filter=lfs diff=lfs merge=lfs -text

.gitignore

@@ -1,3 +1,7 @@
 .Rproj.user
 .Rhistory
 .RData
+doc
+Meta
+/doc/
+/Meta/

.travis.yml

@@ -0,0 +1,111 @@
+# R for travis: see documentation at https://docs.travis-ci.com/user/languages/r
+
+language: r
+r:
+  - bioc-release
+sudo: true
+cache: packages
+bioc_required: true
+bioc_use_devel: true
+warnings_are_errors: false
+
+r_check_args: '--ignore-vignettes --no-examples'
+
+os:
+  - linux
+  - osx
+osx_image: xcode9
+
+addons:
+  apt:
+    packages:
+      - libgdal-dev
+      - libgdal1-dev
+      - libproj-dev
+      - libudunits2-dev
+  brew_packages:
+      - udunits
+
+before_install:
+  - if [ ${TRAVIS_OS_NAME} == linux ]; then sudo add-apt-repository ppa:ubuntugis/ubuntugis-unstable --yes; fi
+  - if [ ${TRAVIS_OS_NAME} == linux ]; then sudo apt-get --yes --force-yes update -qq; fi
+  - if [ ${TRAVIS_OS_NAME} == linux ]; then sudo apt-get install --yes libudunits2-dev libproj-dev libgeos-dev libgdal-dev; fi
+
+
+r_binary_packages:
+  - withr
+  - knitr
+  - crayon
+  - roxygen2
+  - testthat
+  - rex
+  - R6
+  - whisker
+  - jsonlite
+  - httr
+  - RCurl
+  - bitops
+  - DBI
+  - getopt
+  - rjson
+  - snow
+  - RSQLite
+  - base64enc
+  - fastmatch
+  - XML
+  - igraph
+
+
+bioc_packages:
+  - BiocStyle
+  - GenomicRanges
+  - Biobase
+  - affy
+  - EDASeq
+  - edgeR
+  - biomaRt
+  - IRanges
+  - supraHex
+  - S4Vectors
+  - ComplexHeatmap
+  - SummarizedExperiment
+  - BiocGenerics
+  - GenomicFeatures
+  - TxDb.Hsapiens.UCSC.hg19.knownGene
+  - limma
+  - genefilter
+  - ConsensusClusterPlus
+  - pathview
+  - clusterProfiler
+  - BiocCheck
+  - fgsea
+  - GenomicInteractions
+  - GO.db
+  - DO.db
+  - org.Hs.eg.db
+
+r_github_packages:
+  - tiagochst/ELMER.data
+  - hfang-bristol/dnet
+  - BioinformaticsFMRP/TCGAbiolinks
+
+install:
+  - echo 'GITHUB_PAT=15f150aedeaf7dea7ba59ffacb54243b66c10618' > .Renviron
+
+script: 
+  - |
+    travis_wait R CMD build .
+    travis_wait 60 R CMD check ELMER*tar.gz
+
+after_script:
+  - ls -lah
+  - FILE=$(ls -1t *.tar.gz | head -n 1)
+  - Rscript -e "library(BiocCheck); BiocCheck(\"${FILE}\")
+
+r_build_args:  --no-resave-data
+
+notifications:
+    slack: junkdnalab:KV8Dr7etoqqDQPsORdaZLOz2
+    email: false
+    on_success: never # default: change
+    on_failure: always # default: always

DESCRIPTION

@@ -1,8 +1,95 @@
 Package: ELMER
-Title: What the Package Does (one line, title case)
-Version: 0.0.0.9000
-Authors@R: "Lijing Yao <[email protected]> [aut, cre]"
-Description: What the package does (one paragraph)
-Depends: R (>= 3.1.1)
-License: What license is it under?
+Title:
+    Inferring Regulatory Element Landscapes and Transcription Factor
+    Networks Using Cancer Methylomes
+Version: 2.21.0
+Authors@R: c( person("Tiago","Chedraoui Silva", role = c("aut","cre"), email = "[email protected]"),
+           person("Lijing", "Yao", role = "aut", email = "[email protected]"),
+		       person("Simon","Coetzee", role = c("aut"), email = "[email protected]"),
+		       person("Nicole", "Gull", role = "ctb"),
+		       person("Hui", "Shen", role = "ctb"),
+		       person("Peter", "Laird", role = "ctb"),
+		       person("Peggy", "Farnham", role = "aut"),
+		       person("Dechen", "Li", role = "ctb"),
+		       person("Benjamin", "Berman", role = "aut")
+		       )
+Maintainer:
+ Tiago Chedraoui Silva <[email protected]>
+Description: ELMER is designed to use DNA methylation and gene expression from a
+    large number of samples to infere regulatory element landscape and transcription
+    factor network in primary tissue.
+Depends:
+    R (>= 3.4.0),
+    ELMER.data (>= 2.9.3)
+License: GPL-3
 LazyData: true
+VignetteBuilder: knitr
+Imports:
+    GenomicRanges,
+    ggplot2,
+    reshape,
+    grid, 
+    grDevices, 
+    graphics, 
+    methods,
+    parallel, 
+    stats, 
+    utils,
+    IRanges,
+    GenomeInfoDb,
+    S4Vectors,
+    GenomicFeatures,
+    TCGAbiolinks (>= 2.23.7),
+    plyr,
+    Matrix,
+    dplyr,
+    Gviz, 
+    ComplexHeatmap,
+    circlize,
+    MultiAssayExperiment, 
+    SummarizedExperiment,
+    biomaRt, 
+    doParallel,
+    downloader, 
+    ggrepel,
+    lattice, 
+    magrittr, 
+    readr, 
+    scales,
+    rvest,
+    xml2,
+    plotly,
+    gridExtra,
+    rmarkdown,
+    stringr,
+    tibble,
+    tidyr,
+    progress,
+    purrr,
+    reshape2,
+    ggpubr,
+    rtracklayer,
+    DelayedArray
+Suggests:
+    BiocStyle,
+    AnnotationHub,
+    ExperimentHub,
+    knitr,
+    testthat,
+    data.table, 
+    DT,
+    GenomicInteractions,
+    webshot,
+    R.utils,
+    covr,
+    sesameData
+biocViews:
+    DNAMethylation, 
+    GeneExpression, 
+    MotifAnnotation, 
+    Software,
+    GeneRegulation,
+    Transcription, 
+    Network
+Encoding: UTF-8
+RoxygenNote: 7.2.3

ELMER.Rproj

@@ -9,10 +9,10 @@ UseSpacesForTab: Yes
 NumSpacesForTab: 2
 Encoding: UTF-8
 
-RnwWeave: Sweave
+RnwWeave: knitr
 LaTeX: pdfLaTeX
 
 BuildType: Package
 PackageUseDevtools: Yes
 PackageInstallArgs: --no-multiarch --with-keep.source
-PackageRoxygenize: rd,collate,namespace
+PackageRoxygenize: rd