hi, I came across an error in trying to subset a GRangesList with metadata columns on the metadata columns:
> library(GenomicRanges) > grl <- GRangesList(GRanges(),GRanges()) > mcols(grl) <- DataFrame(a=1:2) > mcols(mcols(grl)) <- DataFrame(type="z") > grl[1:2] Error in normalizeSingleBracketSubscript(i, x, byrow = TRUE) : subscript contains NAs or out of bounds indices Calls: [ ... extractROWS -> extractROWS -> normalizeSingleBracketSubscript Also grl[2] produces the same error, while grl[1] does not. traceback and sessionInfo below. thanks, Mike > grl[2] Error in normalizeSingleBracketSubscript(i, x, byrow = TRUE) : subscript contains NAs or out of bounds indices Calls: [ ... extractROWS -> extractROWS -> normalizeSingleBracketSubscript > traceback() 18: stop("subscript contains NAs or out of bounds indices") 17: normalizeSingleBracketSubscript(i, x, byrow = TRUE) 16: extractROWS(x@elementMetadata, i) 15: extractROWS(x@elementMetadata, i) 14: extractROWS(x@elementMetadata, i) 13: extractROWS(x@elementMetadata, i) 12: extractROWS(x, i) 11: extractROWS(x, i) 10: .nextMethod(x, i) 9: eval(expr, envir, enclos) 8: eval(call, callEnv) 7: callNextMethod(x, i) 6: .nextMethod(x = x, i = i) 5: eval(expr, envir, enclos) 4: eval(call, callEnv) 3: callNextMethod(x = x, i = i) 2: grl[2] 1: grl[2] > sessionInfo() R Under development (unstable) (2013-09-12 r63919) Platform: x86_64-apple-darwin12.3.0 (64-bit) 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] parallel stats graphics grDevices utils datasets methods [8] base other attached packages: [1] GenomicRanges_1.13.42 XVector_0.1.2 IRanges_1.19.33 [4] BiocGenerics_0.7.5 knitr_1.2 BiocInstaller_1.11.4 [7] Defaults_1.1-1 loaded via a namespace (and not attached): [1] digest_0.6.3 evaluate_0.4.3 formatR_0.7 stats4_3.1.0 stringr_0.6.2 [6] tools_3.1.0 [[alternative HTML version deleted]] _______________________________________________ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel