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# This GRangePairs directly extends `Pairs` class.
### -----------------------------------------------------------------
### GRangePairs: class
### Exported!
setClass(Class="GRangePairs",
contains="Pairs",
slots=c(first="GRanges",
second="GRanges"),
prototype=list(first=GRanges(),
second=GRanges()
))
setValidity("GRangePairs",
function(object){
x_first <- object@first
x_second <- object@second
## Test first's class
if(class(x_first) != "GRanges")
return("'x@first' must be a GRanges instance")
## test second's class
if(class(x_second) != "GRanges")
return("'x@second' must be a GRanges instance")
return(TRUE)
})
### Formal API:
### GRangePairs(x) - constructor.
### names(x) - NULL or character vector.
### length(x) - single integer N. Nb of pairs in 'x'.
### first(x) - returns "first" slot.
### last(x) - returns "last" slot.
### seqnames(x) - returns DataFrame of seqnames of first, last GRanges.
### strand(x) - returns DataFrame of strands of first, last GRanges.
### seqinfo(x) - returns list of seqinfo of first, last GRanges.
### x[i] - GRangePairs object of the same class as 'x'
### x[[i]] - GRanges object of concatenating the i-th GRangesPairs's
### first, last GRanges.
### unlist(x) - unlist the x into a GRanges object by concatenating
### each pair first.
### grglist(x) - GRangesList object of the same length as 'x'.
### show(x) - compact display in a data.frame-like fashion.
### -----------------------------------------------------------------
### GRangePairs Constructor.
### Exported!
GRangePairs <- function(first=GRanges(), second=GRanges(), ..., names=NULL,
hits=NULL){
if(!is.null(hits)) {
stopifnot(is(hits, "Hits"),
queryLength(hits) == length(first),
subjectLength(hits) == length(second))
first <- first[queryHits(hits)]
second <- second[subjectHits(hits)]
}
if(!(is(first, "GRanges") && is(second, "GRanges")))
stop("'first' and 'second' must be GRanges objects")
stopifnot(length(first) == length(second),
is.null(names) || length(names) == length(first))
if(!missing(...)) {
elementMetadata <- DataFrame(...)
}else{
elementMetadata <- S4Vectors:::make_zero_col_DataFrame(length(first))
}
#rownames(elementMetadata) <- names
new("GRangePairs",first=first, second=second, NAMES=names,
elementMetadata=elementMetadata)
}
### -----------------------------------------------------------------
### GRangePairs getters and setters
### Exported!
setMethod("last", "GRangePairs",
function(x)
{
second(x)
}
)
setMethod("seqnames", "GRangePairs",
function(x){
ans <- DataFrame(first=seqnames(first(x)),
second=seqnames(second(x)))
ans
}
)
setMethod("strand", "GRangePairs",
function(x){
ans <- DataFrame(first=strand(first(x)),
second=strand(second(x)))
ans
}
)
setMethod("seqinfo", "GRangePairs",
function(x) list(seqinfoFirst=seqinfo(first(x)),
seqinfoSecond=seqinfo(second(x)))
)
### - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
### Combine
### Exported!
.unlist_list_of_GRangePairs <- function(x, Class){
metadata <- do.call(rbind, lapply(x, mcols))
rownames(metadata) <- NULL
new(Class, first=do.call(c, lapply(x, first)),
second=do.call(c, lapply(x, second)),
elementMetadata=metadata,
### FIXME: breaks if only some names are NULL
NAMES=unlist(lapply(x, names)))
}
setMethod("c", "GRangePairs",
function(x, ..., recursive=FALSE){
if(isTRUE(recursive))
stop("'recursive' argument not supported")
if (missing(x))
args <- unname(list(...))
else args <- unname(list(x, ...))
.unlist_list_of_GRangePairs(args, class(args[[1]]))
})
### - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
### List methods.
###
### TODO: Remove this method after the definition of the GAlignmentPairs
### class is changed to derive from CompressedList.
setMethod("unlist", "GRangePairs",
function(x, use.names=TRUE)
{
if (!isTRUEorFALSE(use.names))
stop("'use.names' must be TRUE or FALSE")
x_first <- first(x)
x_last <- second(x)
collate_subscript <-
S4Vectors:::make_XYZxyz_to_XxYyZz_subscript(length(x))
ans <- c(x_first, x_last)[collate_subscript]
if (use.names)
names(ans) <- rep(names(x), each=2L)
ans
}
)
### - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
### Coercion.
###
setMethod("grglist", "GRangePairs",
function(x, use.mcols=FALSE)
{
if (!isTRUEorFALSE(use.mcols))
stop("'use.mcols' must be TRUE or FALSE")
x_mcols <- mcols(x)
if (use.mcols && "query.break" %in% colnames(x_mcols))
stop("'mcols(x)' cannot have reserved column \"query.break\"")
x_first <- first(x)
x_last <- second(x)
collate_subscript <-
S4Vectors:::make_XYZxyz_to_XxYyZz_subscript(length(x))
x_unlisted <- c(x_first, x_last)
x_unlisted <- x_unlisted[collate_subscript]
grl <- as(x_unlisted, "GRangesList")
ans <- GenomicAlignments:::shrinkByHalf(grl)
names(ans) <- names(x)
ans_mcols <- DataFrame(query.break=mcols(ans)$nelt1)
if (use.mcols)
ans_mcols <- cbind(ans_mcols, x_mcols)
mcols(ans) <- ans_mcols
ans
}
)
setAs("GRangePairs", "GRangesList",
function(from) grglist(from, use.mcols=TRUE)
)
setAs("GRangePairs", "GRanges",
function(from) unlist(from, use.names=TRUE)
)
### -----------------------------------------------------------------
### swap method for GRangePairs: first becomes last and last becomes first
### Exported!
setGeneric("swap", function(x) standardGeneric("swap"))
setMethod("swap", "GRangePairs", function(x){
BiocGenerics:::replaceSlots(x, first=second(x), second=first(x))
})
### -----------------------------------------------------------------
### unique: keep the unique GRangePairs
### Exported!
setMethod("unique", "GRangePairs", function(x){
duplicatedIndex <- duplicated(paste(paste(first(x)), paste(second(x))))
x[!duplicatedIndex]
})
|
