Hi,
I am currently working with RaggedExperiment. I am interested in selecting only the regions of RaggedExperiment that are included in a GenomicRanges. Despite this functionality is included in the vignette and the manual, I have not been able to apply it to my dataset. It does not work with a toy example either:
library(RaggedExperiment)
library(GenomicRanges)
# Create toy RaggedExperiment
sample1 <- GRanges(c(A = "chr1:1-10:-", B = "chr1:8-14:+", C = "chr2:15-18:+"), score = 3:5)
sample2 <- GRanges(c(D = "chr1:1-10:-", E = "chr2:11-18:+"), score = 1:2)
colDat <- DataFrame(id = 1:2)
ragexp <- RaggedExperiment(sample1 = sample1, sample2 = sample2, colData = colDat)
range <- GRanges("chr1:3-10") subsetByOverlaps(ragexp, range) Error: subscript is a logical vector with out-of-bounds TRUE values traceback() 11: stop(wmsg(...), call. = FALSE) 10: .subscript_error("subscript is a logical vector with out-of-bounds ", "TRUE values") 9: NSBS(i, x, exact = exact, strict.upper.bound = !allow.append, allow.NAs = allow.NAs) 8: NSBS(i, x, exact = exact, strict.upper.bound = !allow.append, allow.NAs = allow.NAs) 7: normalizeSingleBracketSubscript(i, x) 6: extractROWS(x, i) 5: extractROWS(x, i) 4: ranges[xor(o, invert), ] 3: ranges[xor(o, invert), ] 2: subsetByOverlaps(ragexp, range) 1: subsetByOverlaps(ragexp, range)
However, this error is not raised if the range used to subset does not overlap with the RaggedExperiment:
range <- GRanges("chr1:90-100") subsetByOverlaps(ragexp, range) GRanges object with 0 ranges and 0 metadata columns: seqnames ranges strand <Rle> <IRanges> <Rle> ------- seqinfo: 1 sequence from an unspecified genome; no seqlengths
Is there anything I am doing wrong? Thanks,
Carlos
> sessionInfo() R version 3.4.0 (2017-04-21) Platform: x86_64-w64-mingw32/x64 (64-bit) Running under: Windows 7 x64 (build 7601) Service Pack 1 Matrix products: default locale: [1] LC_COLLATE=Spanish_Spain.1252 LC_CTYPE=Spanish_Spain.1252 LC_MONETARY=Spanish_Spain.1252 [4] LC_NUMERIC=C LC_TIME=Spanish_Spain.1252 attached base packages: [1] parallel stats4 stats graphics grDevices utils datasets methods base other attached packages: [1] RaggedExperiment_1.2.3 GenomicRanges_1.30.0 GenomeInfoDb_1.14.0 IRanges_2.12.0 [5] S4Vectors_0.16.0 BiocGenerics_0.24.0 loaded via a namespace (and not attached): [1] lattice_0.20-35 matrixStats_0.52.2 bitops_1.0-6 [4] grid_3.4.0 BiocInstaller_1.28.0 zlibbioc_1.24.0 [7] XVector_0.18.0 Matrix_1.2-11 tools_3.4.0 [10] Biobase_2.38.0 RCurl_1.95-4.8 DelayedArray_0.4.0 [13] compiler_3.4.0 SummarizedExperiment_1.8.0 GenomeInfoDbData_0.99.1