@@ -128,6 +128,7 @@ importFrom(tidyr,pivot_longer)

 importFrom(tidyr,separate_rows)

 importFrom(utils,browseURL)

 importFrom(utils,citation)

+importFrom(utils,data)

 importFrom(utils,read.delim)

 importFrom(utils,sessionInfo)

 importFrom(viridis,viridis)

new file mode 100644

@@ -0,0 +1,40 @@

+#' A sample `DESeqResults` object

+#'

+#' A sample `DESeqResults` object, generated in the `DESeq2` framework

+#'

+#' @details This `DESeqResults` object on the data from the `macrophage` package

+#' has been created comparing IFNg treated samples vs naive samples, accounting

+#' for the different cell lines included.

+#'

+#' Details on how this object has been created are included in the `create_gt_data.R`

+#' script, included in the `scripts` folder of the `GeneTonic` package.

+#'

+#' @references Alasoo, et al. "Shared genetic effects on chromatin and gene

+#' expression indicate a role for enhancer priming in immune response",

+#' Nature Genetics, January 2018 doi: 10.1038/s41588-018-0046-7.

+#'

+#' @name res_macrophage_IFNg_vs_naive

+#' @docType data

+NULL

+

+

+#' A sample `res_enrich` object

+#'

+#' A sample `res_enrich` object, generated with the `topGOtable` function (from

+#' the `pcaExplorer` package).

+#'

+#' @details This `res_enrich` object on the data from the `macrophage` package

+#' has been created by analyzing downstream the differentially expressed genes

+#' when comparing IFNg treated samples vs naive samples, accounting

+#' for the different cell lines included.

+#'

+#' Details on how this object has been created are included in the `create_gt_data.R`

+#' script, included in the `scripts` folder of the `GeneTonic` package.

+#'

+#' @references Alasoo, et al. "Shared genetic effects on chromatin and gene

+#' expression indicate a role for enhancer priming in immune response",

+#' Nature Genetics, January 2018 doi: 10.1038/s41588-018-0046-7.

+#'

+#' @name topgoDE_macrophage_IFNg_vs_naive

+#' @docType data

+NULL

@@ -43,7 +43,7 @@

 #' @importFrom shinyWidgets dropdownButton tooltipOptions

 #' @import SummarizedExperiment

 #' @importFrom tidyr separate_rows pivot_longer

-#' @importFrom utils read.delim sessionInfo browseURL citation

+#' @importFrom utils read.delim sessionInfo browseURL citation data

 #' @importFrom visNetwork renderVisNetwork visIgraph visNetworkOutput visOptions

 #' @importFrom viridis viridis

 #'

new file mode 100644

@@ -0,0 +1,51 @@

+library(GeneTonic)

+library(macrophage)

+data(gse)

+

+# dds object -------------------------------------------------------------------

+library(DESeq2)

+dds_macrophage <- DESeqDataSet(gse, design = ~line + condition)

+rownames(dds_macrophage) <- substr(rownames(dds_macrophage), 1, 15)

+# no need to save this one, can be readily generated

+

+# res object -------------------------------------------------------------------

+keep <- rowSums(counts(dds_macrophage) >= 10) >= 6

+dds_macrophage <- dds_macrophage[keep, ]

+library("org.Hs.eg.db")

+dds_macrophage <- DESeq(dds_macrophage)

+# vst_macrophage <- vst(dds_macrophage)

+res_macrophage_IFNg_vs_naive <- results(dds_macrophage,

+                                        contrast = c("condition", "IFNg", "naive"),

+                                        lfcThreshold = 1, alpha = 0.05)

+res_macrophage_IFNg_vs_naive$SYMBOL <- rowData(dds_macrophage)$SYMBOL

+library("AnnotationDbi")

+# de_symbols_IFNg_vs_naive <- res_macrophage_IFNg_vs_naive[(!(is.na(res_macrophage_IFNg_vs_naive$padj))) & (res_macrophage_IFNg_vs_naive$padj <= 0.05), "SYMBOL"]

+de_symbols_IFNg_vs_naive <- deseqresult2df(res_macrophage_IFNg_vs_naive, FDR = 0.05)$SYMBOL

+bg_ids <- rowData(dds_macrophage)$SYMBOL[rowSums(counts(dds_macrophage)) > 0]

+save(res_macrophage_IFNg_vs_naive, file = "data/res_de_macrophage.RData", compress = "xz")

+

+# res_enrich object ------------------------------------------------------------

+library("topGO")

+topgoDE_macrophage_IFNg_vs_naive <-

+  pcaExplorer::topGOtable(de_symbols_IFNg_vs_naive,

+                          bg_ids,

+                          ontology = "BP",

+                          mapping = "org.Hs.eg.db",

+                          geneID = "symbol",

+                          topTablerows = 500)

+write.table(topgoDE_macrophage_IFNg_vs_naive,

+            "inst/extdata/topgotable_res_IFNg_vs_naive.txt",

+            sep = "\t")

+save(topgoDE_macrophage_IFNg_vs_naive, file = "data/res_enrich_macrophage.RData", compress = "xz")

+topgoDE_macrophage_IFNg_vs_naive <-

+  read.table(system.file("extdata", "topgotable_res_IFNg_vs_naive.txt", package = "GeneTonic"),

+             stringsAsFactors = FALSE)

+

+# annotation object ------------------------------------------------------------

+library("org.Hs.eg.db")

+anno_df <- data.frame(

+  gene_id = rownames(dds_macrophage),

+  gene_name = mapIds(org.Hs.eg.db, keys = rownames(dds_macrophage), column = "SYMBOL", keytype = "ENSEMBL"),

+  stringsAsFactors = FALSE,

+  row.names = rownames(dds_macrophage)

+)

new file mode 100644

@@ -0,0 +1,22 @@

+% Generated by roxygen2: do not edit by hand

+% Please edit documentation in R/GeneTonic-data.R

+\docType{data}

+\name{res_macrophage_IFNg_vs_naive}

+\alias{res_macrophage_IFNg_vs_naive}

+\title{A sample \code{DESeqResults} object}

+\description{

+A sample \code{DESeqResults} object, generated in the \code{DESeq2} framework

+}

+\details{

+This \code{DESeqResults} object on the data from the \code{macrophage} package

+has been created comparing IFNg treated samples vs naive samples, accounting

+for the different cell lines included.

+

+Details on how this object has been created are included in the \code{create_gt_data.R}

+script, included in the \code{scripts} folder of the \code{GeneTonic} package.

+}

+\references{

+Alasoo, et al. "Shared genetic effects on chromatin and gene

+expression indicate a role for enhancer priming in immune response",

+Nature Genetics, January 2018 doi: 10.1038/s41588-018-0046-7.

+}

new file mode 100644

@@ -0,0 +1,24 @@

+% Generated by roxygen2: do not edit by hand

+% Please edit documentation in R/GeneTonic-data.R

+\docType{data}

+\name{topgoDE_macrophage_IFNg_vs_naive}

+\alias{topgoDE_macrophage_IFNg_vs_naive}

+\title{A sample \code{res_enrich} object}

+\description{

+A sample \code{res_enrich} object, generated with the \code{topGOtable} function (from

+the \code{pcaExplorer} package).

+}

+\details{

+This \code{res_enrich} object on the data from the \code{macrophage} package

+has been created by analyzing downstream the differentially expressed genes

+when comparing IFNg treated samples vs naive samples, accounting

+for the different cell lines included.

+

+Details on how this object has been created are included in the \code{create_gt_data.R}

+script, included in the \code{scripts} folder of the \code{GeneTonic} package.

+}

+\references{

+Alasoo, et al. "Shared genetic effects on chromatin and gene

+expression indicate a role for enhancer priming in immune response",

+Nature Genetics, January 2018 doi: 10.1038/s41588-018-0046-7.

+}

similarity index 98%

rename from tests/testthat/setup_genetonic.R

rename to tests/testthat/setuptests_genetonic.R

@@ -52,12 +52,11 @@ dds_macrophage <- dds_macrophage[keep, ]

 dds_unnormalized <- dds_macrophage

 library("org.Hs.eg.db")

-# dds_macrophage <- addIds(dds_macrophage, "SYMBOL")

 dds_macrophage <- DESeq(dds_macrophage)

 vst_macrophage <- vst(dds_macrophage)

 res_macrophage_IFNg_vs_naive <- results(dds_macrophage,

                                         contrast = c("condition", "IFNg", "naive"),

-                                        lfcThreshold = 1, alpha = 0.01)

+                                        lfcThreshold = 1, alpha = 0.05)

 summary(res_macrophage_IFNg_vs_naive)

 res_macrophage_IFNg_vs_naive$SYMBOL <- rowData(dds_macrophage)$SYMBOL