R/generics.R

In wzthu/ATACpipe: An Easy-to-use Systematic pipeline for ATACseq data analysis

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#' @title Get the Fragment objects
#'
#' @param ... Arguments passed to other methods
#' @return Returns a list of \code{\link{Fragment}} objects. If there are
#' no Fragment objects present, returns an empty list.
#' 
#' @keywords internal
#'
#' 
#' @keywords internal
#'
Fragments <- function(object, ...) {
    UseMethod(generic = "Fragments", object = object)
}


#' @title Fragments
#' 
#' @param value A \code{\link{Fragment}} object or list of Fragment objects
#'
#' 
#' @keywords internal
#'
#'
"Fragments<-" <- function(object, ..., value) {
    UseMethod(generic = 'Fragments<-', object = object)
}

#' @title Binarize counts
#'
#' @description 
#' Set counts >1 to 1 in a count matrix
#'
#' @param object A Seurat object
#' @param ... Arguments passed to other methods
#' @return Returns a \code{\link[SeuratObject]{Seurat}} object
#' 
#' @keywords internal
#'
#' @examples
#' print("see https://satijalab.org/signac/reference/binarizecounts")
BinarizeCounts <- function(object, ...) {
    UseMethod(generic = "BinarizeCounts", object = object)
}


#' @title Set and get cell barcode information for a Fragment object
#'
#' @param x A Seurat object
#' @param value A character vector of cell barcodes
#' @param ... Arguments passed to other methods
#' @return cell barcode information
#' 
#' @keywords internal
#'
#' @examples
#' print("see https://satijalab.org/signac/reference/allelefreq")
"Cells<-" <- function(x, ..., value) {
    UseMethod(generic = "Cells<-", object = x)
}



#' @title Get or set links information
#'
#' @description 
#' Get or set the genomic link information for a Seurat object
#'
#' @param ... Arguments passed to other methods
#' @return Links
#'
#' 
#' @keywords internal
#'
#' @examples
#' print("see https://satijalab.org/signac/articles/data_structures.html")
Links <- function(object, ...) {
    UseMethod(generic = "Links", object = object)
}

#' @title Links
#' 
#' @param value A \code{\link[GenomicRanges]{GRanges}} object
#' 
#' @keywords internal
#'
"Links<-" <- function(object, ..., value) {
    UseMethod(generic = "Links<-", object = object)
}

#' @title Region enrichment analysis
#'
#' @description Count fragments within a set of regions for different groups of
#' cells.
#'
#' @param object A Seurat object
#' @param ... Arguments passed to other methods
#' @return Returns a \code{\link[SeuratObject]{Seurat}} object
#' 
#' @keywords internal
#'
#' @examples
#' print("see https://satijalab.org/signac/reference/regionheatmap")
RegionMatrix <- function(object, ...) {
    UseMethod(generic = "RegionMatrix", object = object)
}

#' @title Compute base composition information for genomic ranges
#'
#' @description 
#' Compute the GC content, region lengths, and dinucleotide base frequencies
#' for regions in the assay and add to the feature metadata.
#'
#' @param object A Seurat object, Assay object, or set of genomic ranges
#' @param ... Arguments passed to other methods
#' @return Returns a dataframe
#' 
#' @keywords internal
#'
#' @examples
#' print("see https://satijalab.org/signac/reference/regionstats")
#' 
RegionStats <- function(object, ...) {
    UseMethod(generic = "RegionStats", object = object)
}