version 1.0.0

DESCRIPTION

@@ -0,0 +1,26 @@
+Package: OncoSubtype
+Type: Package
+Title: Predict Cancer Subtypes Based on TCGA Data using Machine
+        Learning Method
+Version: 1.0.0
+Author: Dadong Zhang <dadong.zhang.shared@gmail.com>
+Maintainer: Dadong Zhang <dadong.zhang.shared@gmail.com>
+Description: Provide functionality for cancer subtyping using nearest centroids or machine learning methods based on TCGA data.
+License: GPL-3
+Encoding: UTF-8
+LazyData: true
+RoxygenNote: 7.3.1
+URL: https://github.com/DadongZ/OncoSubtype
+BugReports: https://github.com/DadongZ/OncoSubtype/issues
+Suggests: knitr, rmarkdown, testthat (>= 3.0.0)
+VignetteBuilder: knitr
+LazyDataCompression: xz
+Imports: caret, randomForest, methods, e1071, pheatmap, tibble, dplyr,
+        limma, rlang, Rdpack
+RdMacros: Rdpack
+Depends: SummarizedExperiment, R (>= 3.63),
+Config/testthat/edition: 3
+NeedsCompilation: no
+Packaged: 2024-03-22 16:31:11 UTC; dzhang4
+Repository: CRAN
+Date/Publication: 2024-03-22 17:30:10 UTC

MD5

@@ -0,0 +1,34 @@
+2b420bd8a75c07491fca361edf329211 *DESCRIPTION
+d0e32e1dc27bc82980d0e18a9dfffbab *NAMESPACE
+bf3821c534e3c3c94f5af77f195f004e *R/SubtypeClass.R
+4320f9b2ec39f69299abae003a437fb7 *R/globals.R
+4f4be759a7f7456666ab919852cd9e0b *R/lazy_data.R
+24e1600bf3ac908f5caee4d18557230d *R/main.R
+0c929c3ea3b991684cd92291cbe73179 *README.md
+2aae900b8bbc0b584a6317f5fa91d6e7 *build/partial.rdb
+16156ef58b687a582d05880d25ca1bbb *build/vignette.rds
+0e40c3696b93988d871520a69df69598 *data/example_fpkm.rda
+c650b336c7db6285751a9718ffec7445 *data/hnsc_centroids.rda
+9470b46a5854fd990ef128961aaacce8 *data/luad_centroids.rda
+108f264fa0e059076101078a16ea0220 *data/lusc_centroids.rda
+9c01c006215ef45ac6624ca69ea53a57 *inst/REFERENCES.bib
+9ff5874b74d94a6e0dd05d15fff90791 *inst/doc/OncoSubtype.R
+6fbfea1ec15e29608b5c4b7b0d488db8 *inst/doc/OncoSubtype.Rmd
+c3c33658524f6f9cfa4f5468436d1b41 *inst/doc/OncoSubtype.html
+fc1b5b2696a0e6d51c6124341f142802 *man/PlotHeat.Rd
+c7334b763bf1f1a34109f911001ecd6f *man/SubtypeClass-class.Rd
+2aeadc6d45454a48603b34dd171ac698 *man/centroids_subtype.Rd
+0cd0f6456708bcea3f38ff4223e9cb76 *man/example_fpkm.Rd
+9303da85036d6d8ecb350264047135b2 *man/figures/README-heatmap-1.png
+502a5f8dd6ba90060101596366cb7d58 *man/figures/README-pressure-1.png
+d8b3b9686ac66f2c3403134ba172e53b *man/figures/README-varImp-1.png
+26b2b53f51e42ab63170287bd8fecb73 *man/get_hvg.Rd
+68693a377f71b3c2ae41a0de86d344b3 *man/get_median_centered.Rd
+16d37147354f57da4686dfc1d8cb2017 *man/get_rf_pred.Rd
+771c863c032e37e4de54c388a6f2fc20 *man/hnsc_centroids.Rd
+d6eca82c59ba196a4f55031b2fa2a8e1 *man/load_dataset_from_github.Rd
+ec1586ba4c20e594e5ff0b5901c33f4e *man/luad_centroids.Rd
+027fef571efccb8d7e9c8cf33d012114 *man/lusc_centroids.Rd
+606eb271fc64239015b25f66804fbf96 *man/ml_subtype.Rd
+5aa06b7a405b2a02626bd501d2835959 *tests/test_subtype.R
+6fbfea1ec15e29608b5c4b7b0d488db8 *vignettes/OncoSubtype.Rmd

NAMESPACE

@@ -0,0 +1,30 @@
+# Generated by roxygen2: do not edit by hand
+
+export(PlotHeat)
+export(centroids_subtype)
+export(get_hvg)
+export(get_median_centered)
+export(load_dataset_from_github)
+export(ml_subtype)
+import(Rdpack)
+import(SummarizedExperiment)
+import(caret)
+import(e1071)
+import(pheatmap)
+import(randomForest)
+import(tibble)
+import(utils)
+importFrom(dplyr,arrange)
+importFrom(dplyr,bind_rows)
+importFrom(dplyr,filter)
+importFrom(dplyr,mutate)
+importFrom(dplyr,relocate)
+importFrom(dplyr,select)
+importFrom(limma,removeBatchEffect)
+importFrom(methods,new)
+importFrom(rlang,.data)
+importFrom(stats,cor)
+importFrom(stats,median)
+importFrom(stats,predict)
+importFrom(stats,var)
+importFrom(utils,download.file)

R/SubtypeClass.R

@@ -0,0 +1,10 @@
+#' Set the SubtypeClass
+#'
+#' @return an object of SubtypeClass with three empty solts
+SubtypeClass <- setClass('SubtypeClass', slots = c(features = "character",
+                                    subtypes = "character",
+                                    score = "ANY",
+                                    train_set = "data.frame",
+                                    test_set = "data.frame",
+                                    method = "ANY"),
+                         contains = "character")

R/globals.R

@@ -0,0 +1,5 @@
+#' @import utils
+utils::globalVariables(c("luad_centroids",
+                         "lusc_centroids",
+                         "hnsc_centroids",
+                         "example_fpkm"))

R/lazy_data.R

@@ -0,0 +1,22 @@
+#' @title HNSC predictor centroids
+#'
+#' @description HNSC predictor centroids from \url{https://www.nature.com/articles/nature14129}
+#' @format A \code{tibble} with 728 features and four subtypes.
+"hnsc_centroids"
+
+#' @title LUAD predictor centroids
+#'
+#' @description LUAD predictor centroids from Wilkerson (2012)
+#' @format A \code{tibble} with 506 features and three subtypes bronchioid, magnoid, and squamoid.
+"luad_centroids"
+
+#' @title LUSC predictor centroids
+#'
+#' @description LUSC predictor centroids from Wilkerson (2010)
+#' @format A \code{tibble} with 208 features and four subtypes: primitive, classical, secretory, and basal.
+"lusc_centroids"
+
+#' @title example FPKM data
+#' @description example FPKM data
+#' @format SummarizedExperiment object
+"example_fpkm"