Hello,

I am trying to determine which positions from my data.frame (dmp) are in my GRanges object CpGi. When I call intersect(), R reverts to the base version, even if I use GenomicRanges::intersect(). 

CpGi.sig   <- intersect(dmp, CpGi, ignore.strand=T) 

Error in base::intersect(x, y, ...) : 
  unused argument (ignore.strand = TRUE)

traceback()
3: base::intersect(x, y, ...)
2: GenomicRanges::intersect(dmp, CpGi, ignore.strand = T)
1: GenomicRanges::intersect(dmp, CpGi, ignore.strand = T)


I have also tried using both the development and release versions of GenomicRanges. In both package versions, union, setdiff, and other setOps methods are all being called from base rather than GenomicRanges. 

I tried the parallel version (pintersect()) and received this error:

Error in (function (classes, fdef, mtable)  : 
  unable to find an inherited method for function ‘pintersect’ for signature ‘"data.frame", "GRanges"’

Has anyone seen this problem before? From the help/vignette pages, I thought that data.frames were an acceptable object to use, particularly for pintersect(). 

Any help would be appreciated.

Thanks,

Dana

sessionInfo()
R version 3.3.0 (2016-05-03)
Platform: x86_64-apple-darwin13.4.0 (64-bit)
Running under: OS X 10.11.4 (El Capitan)

locale:
[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] stats4    parallel  stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
[1] BiocInstaller_1.23.5 qvalue_2.4.2         GenomicRanges_1.25.9 GenomeInfoDb_1.8.1  
[5] IRanges_2.7.11       S4Vectors_0.11.9     BiocGenerics_0.19.2 

loaded via a namespace (and not attached):
 [1] Rcpp_0.12.5      plyr_1.8.4       grid_3.3.0       gtable_0.2.0     magrittr_1.5     scales_0.4.0    
 [7] ggplot2_2.1.0    stringi_1.1.1    zlibbioc_1.18.0  reshape2_1.4.1   XVector_0.12.0   splines_3.3.0   
[13] tools_3.3.0      stringr_1.0.0    munsell_0.4.3    colorspace_1.2-6

Try casting your data.frame to a GRanges, e.g., using makeGRangesFromDataFrame().