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### =========================================================================
### refLocsToLocalLocs methods
### =========================================================================
setMethod("refLocsToLocalLocs",
signature("GRanges", "TranscriptDb", "missing"),
function(ranges, txdb, cdsbytx, ...)
{
cdsbytx <- cdsBy(txdb, "tx")
callGeneric(ranges=ranges, cdsbytx=cdsbytx)
})
setMethod("refLocsToLocalLocs",
signature("GRanges", "missing", "GRangesList"),
function(ranges, txdb, cdsbytx, ...)
{
if (is.null(names(cdsbytx)))
stop("the outer list elements of cdsbytx must have ",
" names (i.e., transcript identifiers)")
## cds and protein
cdsGR <- unlist(cdsbytx, use.names=FALSE)
cdsFO <- findOverlaps(ranges, cdsGR, type="within")
cdsid <-
values(unlist(cdsbytx, use.names=FALSE))[["cds_id"]][subjectHits(cdsFO)]
if (is.null(cdsid))
cdsid <- NA_character_
if (length(cdsFO) == 0)
return(GRanges())
nstrand <- as.vector(strand(cdsGR)[subjectHits(cdsFO)] == "-")
qsub <- ranges[queryHits(cdsFO)]
names(qsub) <- names(ranges)[queryHits(cdsFO)]
cds <- .refLocsToCDSLocs(qsub, nstrand, cdsbytx, cdsGR, cdsFO)
pends <- c(ceiling(start(cds)/3), ceiling(end(cds)/3))
protein <- unique(IntegerList(split(pends, rep(seq_len(length(pends)/2)), 2)))
## set strand to match subject overlap
strand(qsub) <- strand(cdsGR[subjectHits(cdsFO)])
txid <- rep(names(cdsbytx), elementLengths(cdsbytx))[subjectHits(cdsFO)]
if (is.null(txid))
txid <- NA_integer_
values(qsub) <- append(values(qsub),
DataFrame(CDSLOC=cds,
PROTEINLOC=protein,
QUERYID=queryHits(cdsFO),
TXID=txid, CDSID=cdsid))
qsub
})
.refLocsToCDSLocs <- function(reflocs, nstrand, grlist, lform, olaps)
{
bounds <- ranges(lform)[subjectHits(olaps)]
## assumption :
## cds regions are sorted 5' to 3' (i.e., cds rank is lowest at 5' end)
cumsums <- .listCumsumShifted(width(grlist))
qrngs <- ranges(reflocs)
if (any(nstrand == FALSE))
qrngs[!nstrand] <- shift(qrngs[!nstrand], - start(bounds)[!nstrand])
if (any(nstrand))
qrngs[nstrand] <- IRanges(end(bounds)[nstrand] - end(qrngs)[nstrand],
width=width(qrngs)[nstrand])
shift(qrngs, 1L + cumsums[subjectHits(olaps)])
}
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