Hi,
On 02/18/2016 03:00 AM, Dario Strbenac wrote:
Good day,
Thank you for these two suggestions. I have questions about both options.
GPos seems to have a limit on the number of bases it can represent. I get an
error: Error in GPos(samplingAreas) : too many genomic positions in 'pos_runs'.
What exactly is this limit ? Could it be added to the documentation ?
It is documented. The man page for GPos says:
Note:
Like for any Vector derivative, the length of a GPos object cannot
exceed ‘.Machine$integer.max’ (i.e. 2^31 on most platforms).
GPos() will return an error if 'pos_runs' contains too many
genomic positions.
I've started to believe that with GPos we might have a use case that is
strong enough to justify adding support for long Vector objects. This
is a big change to our infrastructure though and it won't happen before
the next release.
I used all of the human chromosomes. There is also no documentation of the
sample function for GPos objects.
That's because there is no sample() function for GPos objects:
> sample
function (x, size, replace = FALSE, prob = NULL)
{
if (length(x) == 1L && is.numeric(x) && x >= 1) {
if (missing(size))
size <- x
sample.int(x, size, replace, prob)
}
else {
if (missing(size))
size <- length(x)
x[sample.int(length(x), size, replace, prob)]
}
}
As you can see, sample() works on anything that has a length() and
is subsettable (a.k.a. "vector-like" object). See ?sample for more
information.
H.
Could regioneR be improved to consider strand ? It generates regions with no
strand. I would like the regions to have a strand, since I have a
strand-specific sequencing dataset, and for regions to be possibly chosen on
the opposite strand to a masked region, such as when the genome is masked by
transcripts for the purpose of choosing intergenic sequences.
--------------------------------------
Dario Strbenac
PhD Student
University of Sydney
Camperdown NSW 2050
Australia
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Hervé Pagès
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
E-mail: hpa...@fredhutch.org
Phone: (206) 667-5791
Fax: (206) 667-1319
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