[BioC] GenomicRanges:::.similarSeqnameConvention regular expressions needs some tweaking?
Steve Lianoglou
mailinglist.honeypot at gmail.com
Fri Aug 20 18:53:51 CEST 2010
Hi all,
The GenomicRanges:::.similarSeqnameConvention function is returning
FALSE where, IMHO, it shouldn't be.
I've landed in a situation where this function is called with the
following values for seqs1/2:
seqs1:
[1] "chr1" "chr1_random" "chr10" "chr10_random"
"chr11" "chr11_random"
[7] "chr12" "chr13" "chr13_random" "chr14"
"chr15" "chr15_random"
[13] "chr16" "chr16_random" "chr17" "chr17_random"
"chr18" "chr18_random"
[19] "chr19" "chr19_random" "chr2" "chr2_random"
"chr20" "chr21"
[25] "chr21_random" "chr22" "chr22_random" "chr22_h2_hap1"
"chr3" "chr3_random"
[31] "chr4" "chr4_random" "chr5" "chr5_random"
"chr5_h2_hap1" "chr6"
[37] "chr6_random" "chr6_cox_hap1" "chr6_qbl_hap2" "chr7"
"chr7_random" "chr8"
[43] "chr8_random" "chr9" "chr9_random" "chrM"
"chrX" "chrX_random"
[49] "chrY"
seqs2:
[1] "chrY"
and it looks like the "isArabic" function in funList is the culprit
here. Perhaps this regex test is so necessary, given all the other
tests that are being run?.
I guess it's not so easy to come up w/ a perfect heuristic for this
function to check "comparable seqnames", but IMHO, it seems as if my
scenario should pass as a "good" (ie. the conventions are similar).
Another scenario would be to just have this function return TRUE when
the intersection between seqs1 and seqs2 is length 0. I guess that
must be too simple though ...
--
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
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