Your strand factor only has level "+", but should have levels "+", "-", "*".
Use GenomicRanges::strand() to construct the right thing.
Martin
On 4/14/19, 3:01 AM, "Bioc-devel on behalf of Dario Strbenac"
<bioc-devel-boun...@r-project.org on behalf of dstr7...@uni.sydney.edu.au>
wrote:
Good day,
Although the documentation states "Generally not used directly", I'm trying
it. A small example fails because the input is evaluated to be in the wrong
format, but it doesn't seem so when I look at the variable type of strand.
debug(GAlignments)
GAlignments("chr1", 1L, strand = Rle(factor('+')), cigar = "10M")
debug: new("GAlignments", NAMES = names, seqnames = seqnames,
start = pos, cigar = cigar, strand = strand, elementMetadata =
elementMetadata,
seqinfo = seqinfo)
Browse[2]> strand
factor-Rle of length 1 with 1 run
Lengths: 1
Values : +
Levels(1): +
Browse[2]> n
Error in validObject(.Object) :
invalid class “GAlignments” object: 'strand(x)' must be an unnamed
'factor' Rle with no NAs (and with levels +, - and *)
This looks like a false-positive to me. Also, it would increase readability
if the constructor didn't run off the edge of the PDF page in the reference
manual by using \preformatted. Also, I wonder why seqnames is automatically
converted into a factor Rle, but strand isn't. Couldn't strand also use
.asFactorRle?
--------------------------------------
Dario Strbenac
University of Sydney
Camperdown NSW 2050
Australia
_______________________________________________
Bioc-devel@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/bioc-devel
_______________________________________________
Bioc-devel@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/bioc-devel
