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## Methods for filter classes.
#' @description Extract the field/column name from an AnnotationFilter and
#' ensure that it matches the correct database column name. Depending on
#' whether argument \code{db} is present, the column names are also
#' prefixed with the name of the corresponding table.
#'
#' @param object An \code{AnnotationFilter} object.
#'
#' @param db An \code{EnsDb} object.
#'
#' @param with.tables \code{character} specifying the tables that should be
#' considered when prefixing the column name.
#'
#' @noRd
setMethod("ensDbColumn", "AnnotationFilter",
function(object, db, with.tables = character()) {
clmn <- .fieldInEnsDb(object@field)
if (missing(db))
return(clmn)
if (length(with.tables) == 0)
with.tables <- names(listTables(db))
unlist(prefixColumns(db, clmn, with.tables = with.tables),
use.names = FALSE)
})
setMethod("ensDbColumn", "AnnotationFilterList",
function(object, db, with.tables = character()) {
if (length(object) == 0)
return(character())
unique(unlist(lapply(object, ensDbColumn, db,
with.tables = with.tables)))
})
#' @title Convert an AnnotationFilter to a SQL WHERE condition for EnsDb
#'
#' @aliases convertFilter,AnnotationFilter,EnsDb-method
#' convertFilter,AnnotationFilterList,EnsDb-method
#'
#' @description `convertFilter` converts an `AnnotationFilter::AnnotationFilter`
#' or `AnnotationFilter::AnnotationFilterList` to an SQL where condition
#' for an `EnsDb` database.
#'
#' @note This function *might* be used in direct SQL queries on the SQLite
#' database underlying an `EnsDb` but is more thought to illustrate the
#' use of `AnnotationFilter` objects in combination with SQL databases.
#' This method is used internally to create the SQL calls to the database.
#'
#' @param object `AnnotationFilter` or `AnnotationFilterList` objects (or
#' objects extending these classes).
#'
#' @param db `EnsDb` object.
#'
#' @param with.tables optional `character` vector specifying the names of the
#' database tables that are being queried.
#'
#' @return A `character(1)` with the SQL where condition.
#'
#' @md
#'
#' @rdname convertFilter
#'
#' @author Johannes Rainer
#'
#' @examples
#'
#' library(EnsDb.Hsapiens.v86)
#' edb <- EnsDb.Hsapiens.v86
#'
#' ## Define a filter
#' flt <- AnnotationFilter(~ gene_name == "BCL2")
#'
#' ## Use the method from the AnnotationFilter package:
#' convertFilter(flt)
#'
#' ## Create a combination of filters
#' flt_list <- AnnotationFilter(~ gene_name %in% c("BCL2", "BCL2L11") &
#' tx_biotype == "protein_coding")
#' flt_list
#'
#' convertFilter(flt_list)
#'
#' ## Use the filters in the context of an EnsDb database:
#' convertFilter(flt, edb)
#'
#' convertFilter(flt_list, edb)
setMethod("convertFilter", signature = c(object = "AnnotationFilter",
db = "EnsDb"),
function(object, db, with.tables = character()) {
ensDbQuery(object, db, with.tables)
})
#' @rdname convertFilter
setMethod("convertFilter", signature = c(object = "AnnotationFilterList",
db = "EnsDb"),
function(object, db, with.tables = character()) {
ensDbQuery(object, db, with.tables)
})
#' @description Build the \emph{where} query for an \code{AnnotationFilter} or
#' \code{AnnotationFilterList}.
#'
#' @noRd
setMethod("ensDbQuery", "AnnotationFilter",
function(object, db, with.tables = character()) {
.queryForEnsDbWithTables(object, db, with.tables)
})
setMethod("ensDbQuery", "AnnotationFilterList",
function(object, db, with.tables = character()) {
wq <- NULL
if (length(object)) {
wq <- ensDbQuery(object[[1]], db, with.tables = with.tables)
if (length(object) > 1) {
for (i in 2:length(object)) {
wq <- paste(wq, .logOp2SQL(object@logOp[(i -1)]),
ensDbQuery(object[[i]], db,
with.tables = with.tables))
}
}
## Encapsule all inside brackets.
wq <- paste0("(", wq, ")")
}
wq
})
#' Need an ensDbQuery for SeqNameFilter to support different chromosome naming
#' styles
#'
#' @noRd
setMethod("ensDbQuery", "SeqNameFilter",
function(object, db, with.tables = character()) {
## val <- sQuote(value(object, db))
## Doing all the stuff in here:
vals <- value(object)
clmn <- .fieldInEnsDb(field(object))
if (!missing(db)) {
## o Eventually rename the seqname based on the seqlevelsStyle.
vals <- formatSeqnamesForQuery(db, vals)
if (length(with.tables) == 0)
with.tables <- names(listTables(db))
clmn <- unlist(prefixColumns(db, clmn,
with.tables = with.tables))
}
## o Quote the values.
vals <- sQuote(vals)
## o Concatenate values.
if (length(vals) > 1)
vals <- paste0("(", paste0(vals, collapse = ","), ")")
paste(clmn, .conditionForEnsDb(object), vals)
})
setMethod("ensDbQuery", "SeqStrandFilter",
function(object, db, with.tables = character()) {
## We have to ensure that value is converted to +1, -1.
val <- strand2num(value(object))
clmn <- .fieldInEnsDb(field(object))
if (!missing(db)) {
if (length(with.tables) == 0)
with.tables <- names(listTables(db))
clmn <- unlist(prefixColumns(db, clmn,
with.tables = with.tables))
}
paste(clmn, .conditionForEnsDb(object), val)
})
setMethod("start", signature(x="GRangesFilter"),
function(x, ...){
start(value(x))
})
setMethod("end", signature(x="GRangesFilter"),
function(x, ...){
end(value(x))
})
setMethod("strand", signature(x="GRangesFilter"),
function(x, ...){
as.character(strand(value(x)))
})
#' @description `seqnames`: accessor for the sequence names of the `GRanges`
#' object within a `GRangesFilter`.
#'
#' @param x For `seqnames`, `seqlevels`: a `GRangesFilter` object.
#'
#' @md
#'
#' @rdname Filter-classes
setMethod("seqnames", signature(x="GRangesFilter"),
function(x){
as.character(seqnames(value(x)))
})
#' @description `seqnames`: accessor for the `seqlevels` of the `GRanges`
#' object within a `GRangesFilter`.
#'
#' @md
#'
#' @rdname Filter-classes
setMethod("seqlevels", signature(x="GRangesFilter"),
function(x){
seqlevels(value(x))
})
setMethod("ensDbColumn", "GRangesFilter",
function(object, db, with.tables = character(), ...){
feature <- object@feature
feature <- match.arg(feature, c("gene", "transcript", "exon",
"tx"))
if(object@feature == "transcript")
feature <- "tx"
cols <- c(start = paste0(feature, "_seq_start"),
end = paste0(feature, "_seq_end"),
seqname = "seq_name",
strand = "seq_strand")
if (!missing(db)) {
if (length(with.tables) == 0)
with.tables <- names(listTables(db))
cols <- unlist(prefixColumns(db, cols,
with.tables = with.tables),
use.names = FALSE)
## We have to give the vector the required names!
names(cols) <- 1:length(cols)
names(cols)[grep(cols, pattern = "seq_name")] <- "seqname"
names(cols)[grep(cols, pattern = "seq_strand")] <- "strand"
names(cols)[grep(cols, pattern = "seq_start")] <- "start"
names(cols)[grep(cols, pattern = "seq_end")] <- "end"
}
cols[c("start", "end", "seqname", "strand")]
})
setMethod("ensDbQuery", "GRangesFilter",
function(object, db, with.tables = character()) {
cols <- ensDbColumn(object, db, with.tables)
if (missing(db))
db <- NULL
buildWhereForGRanges(object, cols, db = db)
})
setMethod("ensDbColumn", signature(object = "OnlyCodingTxFilter"),
function(object, db, ...) {
"tx.tx_cds_seq_start"
})
setMethod("ensDbQuery", "OnlyCodingTxFilter",
function(object, db, with.tables = character()) {
"tx.tx_cds_seq_start is not null"
})
setMethod("ensDbColumn", "ProteinIdFilter",
function(object, db, with.tables = character(), ...) {
if (missing(db)) {
return(callNextMethod())
}
if (!hasProteinData(db))
stop("The 'EnsDb' database used does not provide",
" protein annotations! A 'ProteinIdFilter' can not",
" be used.")
callNextMethod()
})
setMethod("ensDbQuery", "ProteinIdFilter",
function(object, db, with.tables = character()) {
if (missing(db))
return(callNextMethod())
if (!hasProteinData(db))
stop("The 'EnsDb' database used does not provide",
" protein annotations! A 'ProteinIdFilter' can not",
" be used.")
.queryForEnsDbWithTables(object, db, with.tables)
})
setMethod("ensDbColumn", "UniprotFilter",
function(object, db, with.tables = character(), ...) {
if (missing(db))
return(callNextMethod())
if (!hasProteinData(db))
stop("The 'EnsDb' database used does not provide",
" protein annotations! A 'UniprotFilter' can not",
" be used.")
callNextMethod()
})
setMethod("ensDbQuery", "UniprotFilter",
function(object, db, with.tables = character()) {
if (missing(db))
return(callNextMethod())
if (!hasProteinData(db))
stop("The 'EnsDb' database used does not provide",
" protein annotations! A 'UniprotFilter' can not",
" be used.")
.queryForEnsDbWithTables(object, db, with.tables)
})
setMethod("ensDbColumn", "ProtDomIdFilter",
function(object, db, with.tables = character(), ...) {
if (missing(db))
return(callNextMethod())
if (!hasProteinData(db))
stop("The 'EnsDb' database used does not provide",
" protein annotations! A 'ProtDomIdFilter' can not",
" be used.")
callNextMethod()
})
setMethod("ensDbQuery", "ProtDomIdFilter",
function(object, db, with.tables = character()) {
if (missing(db))
return(callNextMethod())
if (!hasProteinData(db))
stop("The 'EnsDb' database used does not provide",
" protein annotations! A 'ProtDomIdFilter' can not",
" be used.")
.queryForEnsDbWithTables(object, db, with.tables)
})
setMethod("ensDbColumn", "UniprotDbFilter",
function(object, db, with.tables = character(), ...) {
if (missing(db))
return(callNextMethod())
if (!hasProteinData(db))
stop("The 'EnsDb' database used does not provide",
" protein annotations! A 'UniprotDbFilter' can not",
" be used.")
callNextMethod()
})
setMethod("ensDbQuery", "UniprotDbFilter",
function(object, db, with.tables = character()) {
if (missing(db))
return(callNextMethod())
if (!hasProteinData(db))
stop("The 'EnsDb' database used does not provide",
" protein annotations! A 'ProteinIdFilter' can not",
" be used.")
.queryForEnsDbWithTables(object, db, with.tables)
})
setMethod("ensDbColumn", "UniprotMappingTypeFilter",
function(object, db, with.tables = character(), ...) {
if (missing(db))
return(callNextMethod())
if (!hasProteinData(db))
stop("The 'EnsDb' database used does not provide",
" protein annotations! A 'UniprotMappingTypeFilter' ",
"can not be used.")
callNextMethod()
})
setMethod("ensDbQuery", "UniprotMappingTypeFilter",
function(object, db, with.tables = character()) {
if (missing(db))
return(callNextMethod())
if (!hasProteinData(db))
stop("The 'EnsDb' database used does not provide",
" protein annotations! A 'UniprotMappingTypeFilter' can not",
" be used.")
.queryForEnsDbWithTables(object, db, with.tables)
})
setMethod("ensDbColumn", "TxSupportLevelFilter",
function(object, db, with.tables = character(), ...) {
if (missing(db))
return(callNextMethod())
if (!any(listColumns(db) %in% "tx_support_level"))
stop("The 'EnsDb' database used does not provide",
" transcript support levels! A 'TxSupportLevelFilter' ",
"can not be used.")
callNextMethod()
})
setMethod("ensDbQuery", "TxSupportLevelFilter",
function(object, db, with.tables = character()) {
if (missing(db))
return(callNextMethod())
if (!any(listColumns(db) %in% "tx_support_level"))
stop("The 'EnsDb' database used does not provide",
" transcript support levels! A 'TxSupportLevelFilter' ",
"can not be used.")
.queryForEnsDbWithTables(object, db, with.tables)
})
|
