For sorting the chromosome names in "natural" order, you can use
the makeSeqnameIds() helper function in GenomicRanges:
seqlevels(gr) <- seqlevels(gr)[makeSeqnameIds(seqlevels(gr))]
It recognizes several naming conventions (chr-prefixed or not,
roman, etc...) e.g.:
> makeSeqnameIds(c("Y", "1", "9", "M", "2"))
[1] 4 1 3 5 2
> makeSeqnameIds(c("chrY", "chrI", "chrIX", "chrM", "chrII"))
[1] 4 1 3 5 2
I still need to improve the documentation of this function, put
more examples, and add unit tests. It's used internally by the
makeTranscriptDb* functions in GenomicFeatures to assign internal
ids to the chromosomes so that all the TranscriptDb extractors
can then return GRanges and GRangesList objects with the seqlevels
in the "natural" order.
Cheers,
H.
On 09/17/2013 10:23 AM, Kasper Daniel Hansen wrote:
Actually, what I (and I think several others) just want is
fixSeqnames()
which sorts and fixes them to some convention. I don't really care which
one, but I want to do some easy harmonization, preferably in line with
other bioc tools. I know this is hard to do for all organisms, but having
something that deals with the major ones (human, mouse, fruit fly, yeast,
some monkeys) would be extremely valuable. If this function existed, I
could just throw all my GRanges at it.
Kasper
On Tue, Sep 17, 2013 at 1:14 PM, Michael Lawrence <lawrence.mich...@gene.com
wrote:
When I hit this I usually just do:
seqlevels(gr) <- paste0("chr", c(1:22, "X", "Y"))
It would be nice if there were a function for sorting chromosome names
according to a specified naming convention. Like sortSeqlevels(gr,
UCSCNaming()) or the alternative replacement syntax: seqinfo(gr) <-
sort(seqinfo(gr), UCSCNaming()). Although sort is only single-dispatch.
Michael
On Tue, Sep 17, 2013 at 8:59 AM, Vincent Carey
<st...@channing.harvard.edu>wrote:
I am replying to this as Michael mentions that this is a powerful
operation. Here's my
problem that I believe is related, but I do not see a straightforward
solution
bhmm19uni
GRanges with 559456 ranges and 4 metadata columns:
seqnames ranges strand | name
score
<Rle> <IRanges> <Rle> | <character>
<numeric>
1 chr1 [ 67229025, 67341224] * | 13_Heterochrom/lo
0
2 chr1 [203057955, 203060154] * | 12_Repressed
0
3 chr1 [ 8458427, 8486226] * | 13_Heterochrom/lo
0
4 chr1 [ 16904427, 16904826] * | 5_Strong_Enhancer
0
5 chr1 [ 25289427, 25293426] * | 11_Weak_Txn
0
... ... ... ... ... ...
...
570766 chr22 [51100931, 51101330] * | 2_Weak_Promoter
0
570767 chr22 [51101331, 51101530] * | 6_Weak_Enhancer
0
570768 chr22 [51101531, 51101730] * | 2_Weak_Promoter
0
570769 chr22 [51101731, 51178130] * | 13_Heterochrom/lo
0
570770 chr22 [51178131, 51178330] * | 15_Repetitive/CNV
0
thick numcode
<IRanges> <character>
1 [ 67001613, 67113812] 13
2 [201324578, 201326777] 12
3 [ 8381014, 8408813] 13
4 [ 16777014, 16777413] 5
5 [ 25162014, 25166013] 11
... ... ...
570766 [49447797, 49448196] 2
570767 [49448197, 49448396] 6
570768 [49448397, 49448596] 2
570769 [49448597, 49524996] 13
570770 [49524997, 49525196] 15
---
seqlengths:
chr1 chr10 chr11 chr5 ... chr2 chr21
chr4
249250621 135534747 135006516 180915260 ... 243199373 48129895
191154276
If I try to make a karyogram with ggbio, the chromosomes are in an
unnatural order. What is the right approach to getting the seqinfo in a
natural order with respect to chromosome names and lengths? Reassigning
seqlevels seems dangerous but I haven't experimented fully. It must be a
common use case but I do not see it in doc.
On Tue, May 21, 2013 at 11:00 AM, Michael Lawrence <
lawrence.mich...@gene.com> wrote:
On Mon, May 20, 2013 at 10:36 PM, Hervé Pagès <hpa...@fhcrc.org> wrote:
Michael,
On 05/20/2013 08:44 PM, Michael Lawrence wrote:
On Mon, May 20, 2013 at 4:13 PM, Hervé Pagès <hpa...@fhcrc.org
<mailto:hpa...@fhcrc.org>> wrote:
Hi,
On 05/20/2013 03:15 PM, Michael Lawrence wrote:
On Mon, May 20, 2013 at 3:11 PM, Martin Morgan
<mtmor...@fhcrc.org <mailto:mtmor...@fhcrc.org>> wrote:
Hi Michael --
On 5/20/2013 5:56 AM, Michael Lawrence wrote:
While it's cool that seqlevels<- has become so
flexible,
I still claim
that
rename/keep/drop would be a lot easier to read,
because
they describe the
high-level operation, and there's no reason to
deprecate
them. They're
also
easier to remember. For example, for dropping with
seqlevels<-, the user
needs
to remember that "force" is necessary to drop. Much
easier to just say
"dropSeqlevels(), please". And reimplementing
keepSeqlevels is still too
complicated. Is it such a maintenance burden to have
these simple
wrappers sit
on top of the low-level manipulators?
Another suggestion: renameSeqlevels should not
require
a
named vector (in
cases
where it is unnamed, require that it is parallel to
the
existing
seqlevels, as
with seqlevels<-).
I didn't really indicate what drove my desire to see
keepSeqlevels
deprecated. keepSeqlevels, seqlevels<-, and isActiveSeq
were
developed more
or less independently, and have different contracts. The
different
contracts are confusing to the user, as is creating a
usable
help system
when there are multiple end points for what is a common
operation. The help
pages of each were inadequate in different ways. And
because
the code was
developed independently, support for different objects
was
inconsistent. So
actually, yes, the maintenance (and use) burden for the
previous state of
affairs was substantial.
On the other hand, I agree that keepSeqlevels is
convenient
as a simple
wrapper around seqlevels<-, in the same way that setNames
and names<- are
both useful.
So we could iterate to
keepSeqlevels <-
function(x, value, ...)
{
seqlevels(x, force=TRUE) <- value
x
}
but I'd be less enthusiastic about maintaining the
original
contract of
keepSeqlevels, where keepSeqlevels(gr1, gr2), would have
worked for two
GRanges objects.
Why would this be called keepSeqlevels() if, depending on how
it's
used,
it will either add, drop, rename, or permute the seqlevels?
Couldn't this be called setSeqlevels?
I thought that new2old was necessary for permuting.
The seqlevels setter has no 'new2old' arg.
You're right that
adding should be disallowed for keepSeqlevels(). Adding seqlevels is
not
a common operation. The two common operations are:
* Permuting, usually because the data were imported in non-canonical
order (seqnameStyle was designed to address this, no?).
Permuting is straightforward with seqlevels<-:
> seqlevels(gr)
[1] "chr1" "chr2" "chr3"
> seqlevels(gr) <- rev(seqlevels(gr))
> seqlevels(gr)
[1] "chr3" "chr2" "chr1"
* Subsetting, either by keeping or dropping.
Also straightforward:
> seqlevels(gr, force=TRUE) <- "chr2"
> seqlevels(gr)
[1] "chr2"
Two main reasons: taking a
small slice of the data for prototyping, or removing problematic
chromosomes (sex, circular). This goes back to bsapply and the
exclude
argument.
There are other important use cases:
- Dropping seqlevels that are *not* in use. This happens for example
when subsetting a BAM file with Rsamtools::filterBam to keep only
the alignments located on a given chromosome. The entire sequence
dictionary (in the header) is propagated to the resulting BAM file
so when you read the file with readGAlignments() you end up with a
bunch of useless seqlevels that you generally start by dropping.
You don't want to drop any alignment so force=FALSE is your
friend.
This is sort of tangential to the discussion, but do you really want to
do
this? I would preserve the universe as given by the BAM.
- An even more common operation is renaming: 90% of the times that's
what I use seqlevels<- for, and that's what I tell people to use
when they need to rename their chromosomes. Also straightforward:
> seqlevels(gr)
[1] "chr1" "chr2" "chr3" "chrM"
> seqlevels(gr) <- sub("^chr", "", seqlevels(gr))
> seqlevels(gr)
[1] "1" "2" "3" "M"
> seqlevels(gr)[seqlevels(gr) == "M"] <- "MT"
> seqlevels(gr)
[1] "1" "2" "3" "MT"
Note that this is simpler to use than renameSeqlevels() which
always required you to build the entire right value as a named
vector.
Sure, renaming is a common use case. Not sure how I forgot that.
As I wrote earlier in the thread, renameSeqlevels should be changed so
as
not to require naming of the vector.
So the added-value of keepSeqlevels() seems to boil down to:
(a) it always uses force=TRUE
(b) it preserves the original object and returns the modified object
If you want to restrict the use of keepSeqlevels() to permuting and
dropping, you'll also have to disallow renaming (in addition to
adding).
Then its name will more or less reflect what it does (if "keep" means
"permute" or "drop"). The final result will be something that does
less
than setSeqlevels() and that is not necessarily easier to read: both
will set on the object whatever vector of seqlevels they are supplied,
except that one will fail when doing so would actually result in
adding
or renaming seqlevels.
So it looks like seqlevels<- is pretty powerful. Now I see that if I
scroll
down to the examples in the man page, I find the actual documentation.
It's
cool to learn that we can replace seqlevels on TxDb objects. My argument
has always been that since these low-level operations are so powerful,
it's
nice to have high-level operations to clarify the code. We have to think
hard to know what the RHS will do in that replacement. It's probably one
of
the most complex replacement operations; far more complex than the
typical
one, including levels<- on factor. There's nothing wrong with that; it's
just complexity that we should be able to hide.
Michael
H.
Michael
H.
Well, I wasn't even aware of that feature, so you've made
your
point about
the documentation ;) Sounds like a good compromise to me.
Thanks for understanding,
Michael
Martin
Michael
On Sat, May 18, 2013 at 6:00 PM, Martin Morgan
<mtmor...@fhcrc.org <mailto:mtmor...@fhcrc.org>
<mailto:mtmor...@fhcrc.org <mailto:
mtmor...@fhcrc.org
wrote:
On 05/18/2013 05:42 PM, Martin Morgan wrote:
Some of the most common operations are
straight-forward, e.g.,
> gr = GRanges(paste0("chr", c(1:22,
"X", "Y")), IRanges(1,
100))
> seqlevels(gr) = sub("chr", "ch",
seqlevels(gr))
To get a more comprehensive example I should
have
followed my own
advice and
grabbed from the help page!
## Rename:
seqlevels(txdb) <- sub("chr", "",
seqlevels(txdb))
seqlevels(txdb)
seqlevels(txdb) <- paste0("CH",
seqlevels(txdb))
seqlevels(txdb)
seqlevels(txdb)[seqlevels(__****__txdb)
==
"CHM"] <- "M"
seqlevels(txdb)
--
Computational Biology / Fred Hutchinson Cancer
Research Center
1100 Fairview Ave. N.
PO Box 19024 Seattle, WA 98109
Location: Arnold Building M1 B861
Phone: (206) 667-2793
<tel:%28206%29%20667-2793>
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--
Dr. Martin Morgan, PhD
Fred Hutchinson Cancer Research Center
1100 Fairview Ave. N.
PO Box 19024 Seattle, WA 98109
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Program in Computational Biology
Division of Public Health Sciences
Fred Hutchinson Cancer Research Center
1100 Fairview Ave. N, M1-B514
P.O. Box 19024
Seattle, WA 98109-1024
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