Entering edit mode
Hi all,
I wanted to slice and dice some IRanges object [a] with another [b]:
R> a <- new("IRanges"
, start = c(6407436L, 6407603L, 6410874L, 6422902L, 6423274L,
6423582L,
6427129L, 6428312L, 6431289L, 6434251L, 6434481L, 6439832L, 6440009L,
6442647L, 6442794L)
, width = c(167L, 294L, 193L, 186L, 182L, 131L, 201L, 271L, 450L,
145L,
263L, 79L, 11L, 147L, 798L)
, NAMES = NULL
, elementMetadata = new("DataFrame"
, rownames = NULL
, nrows = 15L
, elementMetadata = NULL
, elementType = "ANY"
, metadata = list()
, listData = structure(list(exon.anno = c("utr5", "cds", "cds",
"cds", "cds",
"cds", "cds", "cds", "cds", "cds", "cds", "cds", "cds", "cds",
"utr3")), .Names = "exon.anno")
)
, elementType = "integer"
, metadata = structure(list(tx.start = 6407435L, tx.end =
6443591L, cds.start = 6407603L,
cds.end = 6442793L), .Names = c("tx.start", "tx.end", "cds.start",
"cds.end"))
)
R> b <- new("IRanges"
, start = c(6407548L, 6410954L, 6410986L, 6423030L, 6423326L,
6427196L,
6427324L, 6428348L, 6428354L, 6428528L, 6431431L, 6431561L, 6434266L,
6439860L, 6443045L, 6443067L, 6443338L)
, width = c(4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L,
4L, 4L,
4L, 4L)
, NAMES = NULL
, elementMetadata = NULL
, elementType = "integer"
, metadata = list()
)
R> setdiff(a, b)
Error in .Method(..., deparse.level = deparse.level) :
no method for coercing this S4 class to a vector
Error in reduce(c(x0, y), drop.empty.ranges = TRUE) :
error in evaluating the argument 'x' in selecting a method for
function 'reduce'
Error in gaps(union(gaps(x, start = start, end = end), y), start =
start, :
error in evaluating the argument 'x' in selecting a method for
function 'gaps'
R> intersect(a,b)
Error in .Method(..., deparse.level = deparse.level) :
no method for coercing this S4 class to a vector
Error in reduce(c(x0, y), drop.empty.ranges = TRUE) :
error in evaluating the argument 'x' in selecting a method for
function 'reduce'
Error in gaps(union(gaps(x, start = start, end = end), y), start =
start, :
error in evaluating the argument 'x' in selecting a method for
function 'gaps'
This had me puzzled for a while until I realized I had a DataFrame
loaded into the elementMetadata of `a` and wondered what the
appropriate behavior for the elementMetadata should be if `a` is split
into more or less pieces (via setdiff or intersect) -- which I didn't
have an answer to.
Nuking the elementMetadata first works just fine:
R> aa <- a
R> elementMetadata(aa) <- NULL
R> setdiff(aa, b)
## works
I don't know what the answer *really* should be as to what the correct
behavior in this situation would be, which I guess could be an
interesting discussion ... perhaps the elementMetadata can be
split/merged with its associated range, or just dropped all together
(perhaps via some explicit parameter in the setdiff, etc. function
call?).
Anyway, in an effort to skirt that rabbit hole for now, could I ask
for a feature request and have IRanges provide a more informative
error message when an end user is gunning at their feet w/ this
scenario? :-)
Thanks,
-steve
--
Steve Lianoglou
Graduate Student: Computational Systems Biology
?| Memorial Sloan-Kettering Cancer Center
?| Weill Medical College of Cornell University
Contact Info: http://cbio.mskcc.org/~lianos/contact
