binilib: Carlo's little helper

# Classes documentation

#' @import tidyverse
#' @import methods
#' @importFrom RColorBrewer brewer.pal
#' @importFrom DESeq2 DESeqDataSetFromMatrix
#' @importFrom DESeq2 estimateSizeFactors
#' @importFrom DESeq2 estimateDispersions
#' @importFrom DESeq2 getVarianceStabilizedData
#' @importFrom fgsea fgsea
NULL

#' @importFrom magrittr %<>%
#' @export
magrittr::`%<>%`

#' The gsea1 class
#'
#' This class contains the results generated by the gsea1T function
#'
#' @docType class
#' @section Slots:
#'    \describe{
#'      \item{\code{ES}:}{numeric value containing the enrichment score}
#'      \item{\code{RS}:}{numeric vector containing the running sum}
#'      \item{\code{signature}:}{named numeric vector containg the gene expression signature}
#'      \item{\code{es_idx}:}{integer indicating the position of the enrichment score}
#'      \item{\code{gs_idx}:}{integers indicating the position the genes from the gene set within the signature}
#'      \item{\code{ledge}:}{character vector of gene names occuring before the ES in the signature}
#'      \item{\code{ledge_index}:}{integer vector of leading edge gene positions}
#'      \item{\code{NES}:}{numeric value containing the enrichment score, will only be filled by gsea_null}
#'      \item{\code{pval}:}{numeric value containing the p-value, will only be filled by gsea_null}
#'      \item{\code{null_es}:}{numeric vector of enrichment scores from a permutation based nullmodel}
#'      \item{\code{mean_nulles}:}{numeric value containing the mean of the relevant tail of null enrichment scores}
#'      }
#' @name gsea1-class
NULL


#' The gsea2 class
#'
#' This class contains the results generated by the gsea2T and the gsea_regulon function, respectively.
#'
#' @docType class
#' @section Slots:
#'    \describe{
#'      \item{\code{signature}:}{named numeric vector containg the gene expression signature}
#'      \item{\code{ES_pos}:}{numeric value containing the enrichment score of gene set 1 (pos. targets)}
#'      \item{\code{ES_neg}:}{numeric value containing the enrichment score of gene set 2 (neg. targets)}
#'      \item{\code{ES_pos_idx}:}{integer value indicating the position of the ES_pos}
#'      \item{\code{ES_neg_idx}:}{integer value indicating the position of the ES_neg}
#'      \item{\code{RS_pos}:}{numeric vector containing the running sum of gene set 1}
#'      \item{\code{RS_neg}:}{numeric vector containing the running sum of gene set 2}
#'      \item{\code{gs_idx_pos}:}{integers indicating the position the genes from the gene set 1 within the signature}
#'      \item{\code{gs_idx_neg}:}{integers indicating the position the genes from the gene set 2 within the signature}
#'      \item{\code{ledge_pos}:}{character vector of gene names from gene set 1 occuring before the ES in the signature}
#'      \item{\code{ledge_neg}:}{character vector of gene names from gene set 2 occuring before the ES in the signature}
#'      \item{\code{ledge_index_pos}:}{integer vector of leading edge gene positions from gene set 1}
#'      \item{\code{ledge_index_neg}:}{integer vector of leading edge gene positions from gene set 2}
#'      \item{\code{null_es_pos}:}{numeric vector of enrichment scores from a permutation based nullmodel for gene set 1}
#'      \item{\code{null_es_neg}:}{numeric vector of enrichment scores from a permutation based nullmodel for gene set 2}
#'      \item{\code{NES_pos}:}{numeric value containing the normalized enrichment score of gene set 1, will only be filled by gsea_null}
#'      \item{\code{NES_neg}:}{numeric value containing the normalized enrichment score of gene set 2, will only be filled by gsea_null}
#'      \item{\code{pval_pos}:}{numeric value containing the p-value of gene set 1, will only be filled by gsea_null}
#'      \item{\code{pval_neg}:}{numeric value containing the p-value of gene set 2, will only be filled by gsea_null}
#'      }
#' @name gsea2-class
NULL