[BioC] findOverlaps method in GenomicRanges not supporting type="equal" for GRangesList, GRangesList?

Nicolas Delhomme nicolas.delhomme at umu.se
Thu Nov 21 13:43:30 CET 2013

Hej Bioc!

When I try to find “equal” ranges from two GRangesList object, I get the following error:

> findOverlaps(query=grng.def,subject=grng.mod,type="equal")
Error in match.arg(type) : 
  'arg' should be one of “any”, “start”, “end”, “within”

Isn’t type=“equal” supported for the GRangesList, GRangesList signature?



R version 3.0.2 (2013-09-25)
Platform: x86_64-apple-darwin13.0.0 (64-bit)

[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8

attached base packages:
[1] parallel  stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
 [1] easyRNASeq_1.8.2       ShortRead_1.20.0       Rsamtools_1.14.1       GenomicRanges_1.14.3   DESeq_1.14.0           lattice_0.20-24        locfit_1.5-9.1        
 [8] Biostrings_2.30.1      XVector_0.2.0          IRanges_1.20.5         edgeR_3.4.0            limma_3.18.3           biomaRt_2.18.0         Biobase_2.22.0        
[15] genomeIntervals_1.18.0 BiocGenerics_0.8.0     intervals_0.14.0      

loaded via a namespace (and not attached):
 [1] annotate_1.40.0      AnnotationDbi_1.24.0 bitops_1.0-6         DBI_0.2-7            genefilter_1.44.0    geneplotter_1.40.0   grid_3.0.2           hwriter_1.3         
 [9] latticeExtra_0.6-26  LSD_2.5              RColorBrewer_1.0-5   RCurl_1.95-4.1       RSQLite_0.11.4       splines_3.0.2        stats4_3.0.2         survival_2.37-4     
[17] tools_3.0.2          XML_3.98-1.1         xtable_1.7-1         zlibbioc_1.8.0

Nicolas Delhomme

Nathaniel Street Lab
Department of Plant Physiology
Umeå Plant Science Center

Tel: +46 90 786 7989
Email: nicolas.delhomme at plantphys.umu.se
SLU - Umeå universitet
Umeå S-901 87 Sweden

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