Browse code

one full round of styler on the codebase, also re-rendering manpages

Federico Marini authored on 27/05/2021 11:22:48
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@@ -30,7 +30,7 @@ NULL
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 #'
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 #' Details on how this object has been created are included in the `create_gt_data.R`
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 #' script, included in the `scripts` folder of the `GeneTonic` package.
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-#' 
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+#'
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 #' @family pathway-analysis-results
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 #'
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 #' @references Alasoo, et al. "Shared genetic effects on chromatin and gene
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 #'
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 #' Details on how this object has been created are included in the `create_gt_data.R`
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 #' script, included in the `scripts` folder of the `GeneTonic` package.
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-#' 
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+#'
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 #' @family pathway-analysis-results
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 #'
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 #' @references Alasoo, et al. "Shared genetic effects on chromatin and gene
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 #'
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 #' Details on how this object has been created are included in the `create_gt_data.R`
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 #' script, included in the `scripts` folder of the `GeneTonic` package.
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-#' 
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+#'
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 #' @family pathway-analysis-results
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 #'
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 #' @references Alasoo, et al. "Shared genetic effects on chromatin and gene
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 #' @name fgseaRes
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 #' @docType data
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 NULL
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Browse code

added info for fgsea output sample data

Federico Marini authored on 28/05/2020 08:15:23
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@@ -90,3 +90,27 @@ NULL
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 #' @docType data
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 NULL
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+
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+#' A sample output from fgsea
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+#'
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+#' A sample output object as created from a call to the `fgsea()` function, in
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+#' the `fgsea` package, as a practical framework for performing GSEA
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+#'
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+#' @details This object has been created on the data from the `macrophage` package
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+#' by analyzing downstream the differentially expressed genes
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+#' when comparing IFNg treated samples vs naive samples, accounting
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+#' for the different cell lines included.
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+#'
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+#' Details on how this object has been created are included in the `create_gt_data.R`
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+#' script, included in the `scripts` folder of the `GeneTonic` package.
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+#'
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+#' @references Alasoo, et al. "Shared genetic effects on chromatin and gene
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+#' expression indicate a role for enhancer priming in immune response",
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+#' Nature Genetics, January 2018 doi: 10.1038/s41588-018-0046-7.
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+#'
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+#' @name fgseaRes
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+#' @docType data
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+NULL
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Browse code

Documenting the sample output from g:Profiler

Federico Marini authored on 26/05/2020 08:34:52
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@@ -30,6 +30,8 @@ NULL
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 #'
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 #' Details on how this object has been created are included in the `create_gt_data.R`
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 #' script, included in the `scripts` folder of the `GeneTonic` package.
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+#' 
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+#' @family pathway-analysis-results
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 #'
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 #' @references Alasoo, et al. "Shared genetic effects on chromatin and gene
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 #' expression indicate a role for enhancer priming in immune response",
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@@ -52,6 +54,8 @@ NULL
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 #'
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 #' Details on how this object has been created are included in the `create_gt_data.R`
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 #' script, included in the `scripts` folder of the `GeneTonic` package.
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+#' 
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+#' @family pathway-analysis-results
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 #'
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 #' @references Alasoo, et al. "Shared genetic effects on chromatin and gene
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 #' expression indicate a role for enhancer priming in immune response",
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-
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-
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+#' A sample output from g:Profiler
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+#'
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+#' A sample output object as created from a call to g:Profiler, with the interface
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+#' provided by `gprofiler2` - using the `gost()` function
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+#'
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+#' @details This object has been created on the data from the `macrophage` package
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+#' by analyzing downstream the differentially expressed genes
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+#' when comparing IFNg treated samples vs naive samples, accounting
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+#' for the different cell lines included.
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+#'
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+#' Details on how this object has been created are included in the `create_gt_data.R`
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+#' script, included in the `scripts` folder of the `GeneTonic` package.
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+#' 
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+#' @family pathway-analysis-results
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+#'
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+#' @references Alasoo, et al. "Shared genetic effects on chromatin and gene
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+#' expression indicate a role for enhancer priming in immune response",
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+#' Nature Genetics, January 2018 doi: 10.1038/s41588-018-0046-7.
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+#'
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+#' @name gostres_macrophage
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+#' @docType data
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+NULL
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Browse code

Documenting data object from Enrichr

Federico Marini authored on 26/05/2020 08:31:01
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@@ -38,3 +38,31 @@ NULL
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 #' @name topgoDE_macrophage_IFNg_vs_naive
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 #' @docType data
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 NULL
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+
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+
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+#' A sample output from Enrichr
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+#'
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+#' A sample output object as created from a call to Enrichr, with the interface
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+#' provided by `enrichR` - using the `enrichr()` function
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+#'
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+#' @details This object has been created on the data from the `macrophage` package
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+#' by analyzing downstream the differentially expressed genes
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+#' when comparing IFNg treated samples vs naive samples, accounting
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+#' for the different cell lines included.
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+#'
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+#' Details on how this object has been created are included in the `create_gt_data.R`
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+#' script, included in the `scripts` folder of the `GeneTonic` package.
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+#'
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+#' @references Alasoo, et al. "Shared genetic effects on chromatin and gene
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+#' expression indicate a role for enhancer priming in immune response",
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+#' Nature Genetics, January 2018 doi: 10.1038/s41588-018-0046-7.
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+#'
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+#' @name enrichr_output_macrophage
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+#' @docType data
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+NULL
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+
Browse code

Added data docs, edited setup file in test suite. Also added script for generating the RData objects

Federico Marini authored on 29/11/2019 10:09:32
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+#' A sample `DESeqResults` object
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+#'
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+#' A sample `DESeqResults` object, generated in the `DESeq2` framework
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+#'
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+#' @details This `DESeqResults` object on the data from the `macrophage` package
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+#' has been created comparing IFNg treated samples vs naive samples, accounting
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+#' for the different cell lines included.
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+#'
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+#' Details on how this object has been created are included in the `create_gt_data.R`
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+#' script, included in the `scripts` folder of the `GeneTonic` package.
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+#'
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+#' @references Alasoo, et al. "Shared genetic effects on chromatin and gene
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+#' expression indicate a role for enhancer priming in immune response",
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+#' Nature Genetics, January 2018 doi: 10.1038/s41588-018-0046-7.
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+#'
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+#' @name res_macrophage_IFNg_vs_naive
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+#' @docType data
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+NULL
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+
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+
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+#' A sample `res_enrich` object
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+#'
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+#' A sample `res_enrich` object, generated with the `topGOtable` function (from
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+#' the `pcaExplorer` package).
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+#'
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+#' @details This `res_enrich` object on the data from the `macrophage` package
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+#' has been created by analyzing downstream the differentially expressed genes
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+#' when comparing IFNg treated samples vs naive samples, accounting
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+#' for the different cell lines included.
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+#'
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+#' Details on how this object has been created are included in the `create_gt_data.R`
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+#' script, included in the `scripts` folder of the `GeneTonic` package.
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+#'
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+#' @references Alasoo, et al. "Shared genetic effects on chromatin and gene
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+#' expression indicate a role for enhancer priming in immune response",
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+#' Nature Genetics, January 2018 doi: 10.1038/s41588-018-0046-7.
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+#'
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+#' @name topgoDE_macrophage_IFNg_vs_naive
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+#' @docType data
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+NULL