#' @include generics.R
#' @importFrom methods callGeneric
#' @importFrom SeuratObject DefaultAssay
#' @importFrom GenomeInfoDb
#' seqinfo seqinfo<-
#' seqnames seqnames<-
#' seqlevels seqlevels<-
#' sortSeqlevels
#' seqlengths seqlengths<-
#' isCircular isCircular<-
#' genome genome<-
NULL
setOldClass(Classes = "ChromatinAssay")
# TODO add keepSeqlevels, dropSeqlevels, renameSeqlevels, etc
#' Access and modify sequence information for ChromatinAssay objects
#'
#' Methods for accessing and modifying
#' \code{\link[GenomeInfoDb]{Seqinfo}} object information stored in a
#' \code{\link{ChromatinAssay}} object.
#'
#' @name seqinfo-methods
#' @param x A \code{\link{ChromatinAssay}} object
#'
#' @aliases seqinfo seqinfo,ChromatinAssay-method
#' @seealso
#' \itemize{
#' \item{\link[GenomeInfoDb]{seqinfo} in the \pkg{GenomeInfoDb} package.}
#' \item{\link{ChromatinAssay-class}}
#' }
#' @exportMethod seqinfo
#' @concept seqinfo
setMethod(
f = "seqinfo",
signature = "ChromatinAssay",
definition = function(x) {
slot(object = x, name = "seqinfo")
}
)
#' @param value A \code{\link[GenomeInfoDb]{Seqinfo}} object or name of a UCSC
#' genome to store in the \code{\link{ChromatinAssay}}
#' @describeIn seqinfo-methods set method for ChromatinAssay objects
#' @exportMethod seqinfo<-
#' @concept seqinfo
setMethod(
f = "seqinfo<-",
signature = "ChromatinAssay",
definition = function(
x,
value
) {
x <- SetAssayData(object = x, layer = "seqinfo", new.data = value)
x
}
)
#' @aliases seqlevels
#' @describeIn seqinfo-methods get method for ChromatinAssay objects
#' @exportMethod seqlevels
#' @concept seqinfo
setMethod(
f = "seqlevels",
signature = "ChromatinAssay",
definition = function(x) {
x <- seqinfo(x = x)
if (is.null(x = x)) {
return(NULL)
} else {
callGeneric()
}
}
)
#' @describeIn seqinfo-methods set method for ChromatinAssay objects
#' @exportMethod seqlevels<-
#' @concept seqinfo
setMethod(
f = "seqlevels<-",
signature = "ChromatinAssay",
definition = function(
x, value
) {
sinfo <- seqinfo(x = x)
seqlevels(x = sinfo) <- value
x <- SetAssayData(object = x, layer = "seqinfo", new.data = sinfo)
return(x)
}
)
#' @aliases seqnames
#' @describeIn seqinfo-methods get method for ChromatinAssay objects
#' @exportMethod seqnames
#' @concept seqinfo
setMethod(
f = "seqnames",
signature = "ChromatinAssay",
definition = function(x) {
x <- seqinfo(x = x)
if (is.null(x = x)) {
return(NULL)
} else {
callGeneric()
}
}
)
#' @describeIn seqinfo-methods set method for ChromatinAssay objects
#' @exportMethod seqnames<-
#' @concept seqinfo
setMethod(
f = "seqnames<-",
signature = "ChromatinAssay",
definition = function(
x, value
) {
sinfo <- seqinfo(x = x)
seqnames(x = sinfo) <- value
x <- SetAssayData(object = x, layer = "seqinfo", new.data = sinfo)
return(x)
}
)
#' @aliases seqlengths
#' @describeIn seqinfo-methods get method for ChromatinAssay objects
#' @exportMethod seqlengths
#' @concept seqinfo
setMethod(
f = "seqlengths",
signature = "ChromatinAssay",
definition = function(x) {
x <- seqinfo(x = x)
if (is.null(x = x)) {
return(NULL)
} else {
if (is.null(x = x)) {
return(NULL)
} else {
callGeneric()
}
}
}
)
#' @describeIn seqinfo-methods set method for ChromatinAssay objects
#' @exportMethod seqlengths<-
#' @concept seqinfo
setMethod(
f = "seqlengths<-",
signature = "ChromatinAssay",
definition = function(
x, value
) {
sinfo <- seqinfo(x = x)
seqlengths(x = sinfo) <- value
x <- SetAssayData(object = x, layer = "seqinfo", new.data = sinfo)
return(x)
}
)
#' @aliases genome
#' @describeIn seqinfo-methods get method for ChromatinAssay objects
#' @exportMethod genome
#' @concept seqinfo
setMethod(
f = "genome",
signature = "ChromatinAssay",
definition = function(x) {
x <- seqinfo(x = x)
if (is.null(x = x)) {
return(NULL)
} else {
callGeneric()
}
}
)
#' @describeIn seqinfo-methods set method for ChromatinAssay objects
#' @importFrom SeuratObject SetAssayData
#' @exportMethod genome<-
#' @concept seqinfo
setMethod(
f = "genome<-",
signature = "ChromatinAssay",
definition = function(
x, value
) {
x <- SetAssayData(object = x, layer = "seqinfo", new.data = value)
return(x)
}
)
#' @aliases isCircular
#' @describeIn seqinfo-methods get method for ChromatinAssay objects
#' @exportMethod isCircular
#' @concept seqinfo
setMethod(
f = "isCircular",
signature = "ChromatinAssay",
definition = function(x) {
x <- seqinfo(x = x)
if (is.null(x = x)) {
return(NULL)
} else {
callGeneric()
}
}
)
#' @describeIn seqinfo-methods set method for ChromatinAssay objects
#' @exportMethod isCircular<-
#' @concept seqinfo
setMethod(
f = "isCircular<-",
signature = "ChromatinAssay",
definition = function(
x, value
) {
sinfo <- seqinfo(x = x)
isCircular(x = sinfo) <- value
x <- SetAssayData(object = x, layer = "seqinfo", new.data = sinfo)
return(x)
}
)
#' @describeIn seqinfo-methods get method for Seurat objects
#' @concept seqinfo
setMethod(
f = "seqinfo",
signature = "Seurat",
definition = function(x) {
assay <- DefaultAssay(object = x)
slot(object = x[[assay]], name = "seqinfo")
}
)
#' @describeIn seqinfo-methods set method for Seurat objects
#' @concept seqinfo
setMethod(
f = "seqinfo<-",
signature = "Seurat",
definition = function(
x,
value
) {
assay <- DefaultAssay(object = x)
seqinfo(x = x[[assay]]) <- value
x
}
)
#' @describeIn seqinfo-methods get method for Seurat objects
#' @concept seqinfo
setMethod(
f = "seqlevels",
signature = "Seurat",
definition = function(x) {
x <- seqinfo(x = x)
if (is.null(x = x)) {
return(NULL)
} else {
callGeneric()
}
}
)
#' @describeIn seqinfo-methods set method for Seurat objects
#' @concept seqinfo
setMethod(
f = "seqlevels<-",
signature = "Seurat",
definition = function(
x, value
) {
assay <- DefaultAssay(object = x)
seqlevels(x = x[[assay]]) <- value
x
}
)
#' @describeIn seqinfo-methods get method for Seurat objects
#' @concept seqinfo
setMethod(
f = "seqnames",
signature = "Seurat",
definition = function(x) {
x <- seqinfo(x = x)
if (is.null(x = x)) {
return(NULL)
} else {
callGeneric()
}
}
)
#' @describeIn seqinfo-methods set method for Seurat objects
#' @concept seqinfo
setMethod(
f = "seqnames<-",
signature = "Seurat",
definition = function(
x, value
) {
assay <- DefaultAssay(object = x)
seqnames(x = x[[assay]]) <- value
x
}
)
#' @describeIn seqinfo-methods get method for Seurat objects
#' @concept seqinfo
setMethod(
f = "seqlengths",
signature = "Seurat",
definition = function(x) {
x <- seqinfo(x = x)
if (is.null(x = x)) {
return(NULL)
} else {
callGeneric()
}
}
)
#' @describeIn seqinfo-methods set method for Seurat objects
#' @concept seqinfo
setMethod(
f = "seqlengths<-",
signature = "Seurat",
definition = function(
x, value
) {
assay <- DefaultAssay(object = x)
seqlengths(x = x[[assay]]) <- value
x
}
)
#' @describeIn seqinfo-methods get method for Seurat objects
#' @concept seqinfo
setMethod(
f = "genome",
signature = "Seurat",
definition = function(x) {
x <- seqinfo(x = x)
if (is.null(x = x)) {
return(NULL)
} else {
callGeneric()
}
}
)
#' @describeIn seqinfo-methods set method for Seurat objects
#' @importFrom SeuratObject SetAssayData
#' @concept seqinfo
setMethod(
f = "genome<-",
signature = "Seurat",
definition = function(
x, value
) {
x <- SetAssayData(object = x, layer = "seqinfo", new.data = value)
}
)
#' @describeIn seqinfo-methods get method for Seurat objects
#' @concept seqinfo
setMethod(
f = "isCircular",
signature = "Seurat",
definition = function(x) {
x <- seqinfo(x = x)
if (is.null(x = x)) {
return(NULL)
} else {
callGeneric()
}
}
)
#' @describeIn seqinfo-methods set method for Seurat objects
#' @concept seqinfo
setMethod(
f = "isCircular<-",
signature = "Seurat",
definition = function(
x, value
) {
assay <- DefaultAssay(object = x)
isCircular(x = x[[assay]]) <- value
x
}
)
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