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## Deprecated functions.
#' @aliases ensembldb-deprecated
#'
#' @title Deprecated functionality
#'
#' @description All functions, methods and classes listed on this page are
#' deprecated and might be removed in future releases.
#'
#' @param value The value for the filter.
#' @param condition The condition for the filter.
#'
#' @name Deprecated
NULL
#> NULL
#' @description \code{GeneidFilter} creates a \code{GeneIdFilter}. Use
#' \code{GeneIdFilter} from the \code{AnnotationFilter} package instead.
#'
#' @rdname Deprecated
GeneidFilter <- function(value, condition = "==") {
.Deprecated("GeneIdFilter")
if (missing(value))
stop("A filter without a value makes no sense!")
## if(length(value) > 1){
## if(condition=="=")
## condition="in"
## if(condition=="!=")
## condition="not in"
## }
return(new("GeneIdFilter", condition = condition,
value = as.character(value), field = "gene_id"))
}
#' @description \code{GenebiotypeFilter} creates a \code{GeneBiotypeFilter}. Use
#' \code{GeneBiotypeFilter} from the \code{AnnotationFilter} package instead.
#'
#' @rdname Deprecated
GenebiotypeFilter <- function(value, condition = "=="){
.Deprecated("GeneBiotypeFilter")
if(missing(value))
stop("A filter without a value makes no sense!")
return(new("GeneBiotypeFilter", condition = condition,
value = as.character(value), field = "gene_biotype"))
}
#' @description \code{EntrezidFilter} creates a \code{EntrezFilter}. Use
#' \code{EntrezFilter} from the \code{AnnotationFilter} package instead.
#'
#' @rdname Deprecated
EntrezidFilter <- function(value, condition = "=="){
.Deprecated("EntrezFilter")
if(missing(value))
stop("A filter without a value makes no sense!")
return(new("EntrezFilter", condition = condition,
value = as.character(value), field = "entrez"))
}
#' @description \code{TxidFilter} creates a \code{TxIdFilter}. Use
#' \code{TxIdFilter} from the \code{AnnotationFilter} package instead.
#'
#' @rdname Deprecated
TxidFilter <- function(value, condition = "=="){
.Deprecated("TxIdFilter")
if(missing(value))
stop("A filter without a value makes no sense!")
return(new("TxIdFilter", condition = condition,
value = as.character(value), field = "tx_id"))
}
#' @description \code{TxbiotypeFilter} creates a \code{TxBiotypeFilter}. Use
#' \code{TxBiotypeFilter} from the \code{AnnotationFilter} package instead.
#'
#' @rdname Deprecated
TxbiotypeFilter <- function(value, condition="=="){
.Deprecated("TxBiotypeFilter")
if(missing(value))
stop("A filter without a value makes no sense!")
return(new("TxBiotypeFilter", condition=condition,
value=as.character(value), field = "tx_biotype"))
}
#' @description \code{ExonidFilter} creates a \code{ExonIdFilter}. Use
#' \code{ExonIdFilter} from the \code{AnnotationFilter} package instead.
#'
#' @rdname Deprecated
ExonidFilter <- function(value, condition="=="){
.Deprecated("ExonIdFilter")
if(missing(value))
stop("A filter without a value makes no sense!")
return(new("ExonIdFilter", condition=condition,
value=as.character(value), field = "exon_id"))
}
#' @description \code{ExonrankFilter} creates a \code{ExonRankFilter}. Use
#' \code{ExonRankFilter} from the \code{AnnotationFilter} package instead.
#'
#' @rdname Deprecated
ExonrankFilter <- function(value, condition="=="){
.Deprecated("ExonRankFilter")
if(missing(value))
stop("A filter without a value makes no sense!")
return(new("ExonRankFilter", condition=condition, value=as.integer(value),
field = "exon_rank"))
}
#' @description \code{SeqNameFilter} creates a \code{SeqNameFilter}. Use
#' \code{SeqNameFilter} from the \code{AnnotationFilter} package instead.
#'
#' @rdname Deprecated
SeqnameFilter <- function(value, condition="=="){
.Deprecated("SeqNameFilter")
if(missing(value))
stop("A filter without a value makes no sense!")
return(new("SeqNameFilter", condition=condition, value=as.character(value),
field = "seq_name"))
}
#' @description \code{SeqstrandFilter} creates a \code{SeqStrandFilter}. Use
#' \code{SeqStrandFilter} from the \code{AnnotationFilter} instead.
#'
#' @rdname Deprecated
SeqstrandFilter <- function(value, condition="=="){
.Deprecated("SeqStrandFilter")
if(missing(value)){
stop("A filter without a value makes no sense!")
}
## checking value: should be +, -, will however be translated to -1, 1
if(class(value)=="character"){
value <- match.arg(value, c("1", "-1", "+1", "-", "+"))
if(value=="-")
value <- "-1"
if(value=="+")
value <- "+1"
## OK, now transforming to number
value <- as.numeric(value)
}
if(!(value==1 | value==-1))
stop("The strand has to be either 1 or -1 (or \"+\" or \"-\")")
return(new("SeqStrandFilter", condition=condition, value=as.character(value),
field = "seq_strand"))
}
#' @description
#'
#' \code{SeqstartFilter} creates a \code{GeneStartFilter}, \code{TxStartFilter}
#' or \code{ExonStartFilter} depending on the value of the parameter
#' \code{feature}. Use \code{GeneStartFilter}, \code{TxStartFilter} and
#' \code{ExonStartFilter} instead.
#'
#' @param feature For \code{SeqstartFilter} and \code{SeqendFilter}: on what type
#' of feature should the filter be applied? Supported are \code{"gene"},
#' \code{"tx"} and \code{"exon"}.
#'
#' @rdname Deprecated
SeqstartFilter <- function(value, condition=">", feature="gene"){
.Deprecated(msg = paste0("The use of 'SeqstartFilter' is deprecated. Use ",
"one of 'GeneStartFilter', 'ExonStartFilter'",
" or 'TxStartFilter' instead."))
feature <- match.arg(feature, c("gene", "exon", "tx"))
return(new(paste0(sub("^([[:alpha:]])", "\\U\\1", feature, perl=TRUE),
"StartFilter"), value = as.integer(value),
condition = condition,
field = paste0(feature, "_start")))
}
#' @description
#'
#' \code{SeqendFilter} creates a \code{GeneEndFilter}, \code{TxEndFilter}
#' or \code{ExonEndFilter} depending on the value of the parameter
#' \code{feature}. Use \code{GeneEndFilter}, \code{TxEndFilter} and
#' \code{ExonEndFilter} instead.
#'
#' @rdname Deprecated
SeqendFilter <- function(value, condition="<", feature="gene"){
.Deprecated(msg = paste0("The use of 'SeqendFilter' is deprecated. Use ",
"one of 'GeneEndFilter', 'ExonEndFilter'",
" or 'TxEndFilter' instead."))
feature <- match.arg(feature, c("gene", "exon", "tx"))
return(new(paste0(sub("^([[:alpha:]])", "\\U\\1", feature, perl=TRUE)),
"EndFilter"), value = as.integer(value),
condition = condition,
field = paste0(feature, "_end"))
}
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