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   

Hi Carlos,

Thank you for your report. This is indeed a bug in the subsetByOverlaps,RaggedExperiment,Vector-method.

This was fixed in version 1.2.4 in release and 1.3.7  in devel.

Regards,

Marcel