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AllGenerics.R
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AllGenerics.R
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## ###################################################################
## ###################################################################
## constructor methods
#' @export
#' @rdname concomp-class
setGeneric("concomp",
valueClass="concomp",
function(obj, ...) standardGeneric("concomp"))
## ###################################################################
## ###################################################################
## plot methods
#' @export
#' @rdname splicegrahm
#' @docType methods
setGeneric("splicegrahm",
function(obj, sort_sep = FALSE, sort_idx = 1,
log_base = 10, log_shift = 1, bin = TRUE,
genomic = TRUE, ex_use = 2/3, flip_neg = TRUE,
j_incl = FALSE, highlight = NULL,
use_blk = FALSE, eps = 1e4, txlist = NULL,
txdb = NULL, orgdb = NULL, title="", ...)
standardGeneric("splicegrahm"))
#' @export
#' @rdname splicegrahm2
#' @docType methods
setGeneric("splicegrahm2",
function(obj1, obj2, sort_sep = FALSE,
sort_idx1 = 1, sort_idx2 = 1,
log_base = 10, log_shift = 1, bin = TRUE,
genomic = TRUE, ex_use = 2/3, flip_neg = TRUE,
j_incl = FALSE, use_blk = FALSE, eps = 1e4,
txlist = NULL, txdb = NULL, orgdb = NULL, title="",
mirror = TRUE, same_scale = TRUE, ...)
standardGeneric("splicegrahm2"))
#' @export
#' @docType methods
#' @rdname splicegralp
setGeneric("splicegralp",
function(obj, e_loads, j_loads = NULL, load_lims = NULL,
genomic = TRUE, ex_use = 2/3,
flip_neg = TRUE, use_blk = FALSE,
txlist = NULL, txdb = NULL,
orgdb = NULL,...)
standardGeneric("splicegralp"))
#' @export
#' @docType methods
#' @rdname splicepca
setGeneric("splicepca",
function(obj, npc = 3, pc_sep = TRUE, ej_w = c(1, 1),
log_base = 10, log_shift = 1,
genomic = TRUE, ex_use = 2/3,
flip_neg = TRUE, use_blk = FALSE,
txlist = NULL, txdb = NULL,
orgdb = NULL, scores = FALSE,
plot = TRUE, ...)
standardGeneric("splicepca"))
#' @export
#' @docType methods
#' @rdname splicepcp
setGeneric("splicepcp",
function(obj, log_base = 10, log_shift = 1, genomic = TRUE,
ex_use = 2/3, flip_neg = TRUE, imodel = TRUE,
highlight = NULL, eps = 1e4,
txlist = NULL, txdb = NULL, orgdb = NULL, ...)
standardGeneric("splicepcp"))
## ###################################################################
## ###################################################################
## getter methods
#' @export
#' @rdname slots-generic
setGeneric("eRanges", function(object) standardGeneric("eRanges"))
#' @export
#' @rdname slots-generic
setGeneric("jRanges", function(object) standardGeneric("jRanges"))
#' @export
#' @rdname slots-generic
setGeneric("eCoverage", function(object) standardGeneric("eCoverage"))
#' @export
#' @rdname slots-generic
setGeneric("jCoverage", function(object) standardGeneric("jCoverage"))
## ###################################################################
## ###################################################################
## setter methods
#' @export
#' @rdname slots-generic
setGeneric("eRanges<-", function(object, ..., value) standardGeneric("eRanges<-"))
#' @export
#' @rdname slots-generic
setGeneric("jRanges<-", function(object, ..., value) standardGeneric("jRanges<-"))
#' @export
#' @rdname slots-generic
setGeneric("eCoverage<-", function(object, ..., value) standardGeneric("eCoverage<-"))
#' @export
#' @rdname slots-generic
setGeneric("jCoverage<-", function(object, ..., value) standardGeneric("jCoverage<-"))