R/GeneTonic-data.R
9c3a5f11
 #' 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.
fc8e87b6
 #'
8fb5de41
 #' @family pathway-analysis-results
9c3a5f11
 #'
 #' @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
198fef13
 
 
 #' A sample output from Enrichr
 #'
 #' A sample output object as created from a call to Enrichr, with the interface
 #' provided by `enrichR` - using the `enrichr()` function
 #'
 #' @details This object has been created on the data from the `macrophage` package
 #' 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.
fc8e87b6
 #'
8fb5de41
 #' @family pathway-analysis-results
198fef13
 #'
 #' @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 enrichr_output_macrophage
 #' @docType data
 NULL
 
 
 
8fb5de41
 #' A sample output from g:Profiler
 #'
 #' A sample output object as created from a call to g:Profiler, with the interface
 #' provided by `gprofiler2` - using the `gost()` function
 #'
 #' @details This object has been created on the data from the `macrophage` package
 #' 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.
fc8e87b6
 #'
8fb5de41
 #' @family pathway-analysis-results
 #'
 #' @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 gostres_macrophage
 #' @docType data
 NULL
198fef13
 
0d8b56c8
 
 #' A sample output from fgsea
 #'
 #' A sample output object as created from a call to the `fgsea()` function, in
 #' the `fgsea` package, as a practical framework for performing GSEA
 #'
 #' @details This object has been created on the data from the `macrophage` package
 #' 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 fgseaRes
 #' @docType data
 NULL