Hi,
I have question about summarizeOverlaps when set reads as a GRangesList object. In the Usage section, there is no method for signature 'GRanges,GRangesList'. However, in the arguments section, it is said that GRangesList could be the input of reads. Then I tried codes like this,
library(GenomicAlignments) tg <- GRanges("chr1", IRanges(c(1, 101, 201), width=100)) reads <- GRangesList(A=GRanges("chr1", IRanges(1:100, width=10))) tc <- summarizeOverlaps(features=tg, reads=reads) assays(tc)[[1]] reads [1,] 0 [2,] 0 [3,] 0
tc2 <- summarizeOverlaps(features=tg, reads=reads$A)
assays(tc2)[[1]]
reads
[1,] 91
[2,] 0
[3,] 0
I hope summarizeOverlaps could accept GRangesList as inputs for reads. Is there anything I missed? Thank you.
Here is my sessionInfo
R version 3.3.2 (2016-10-31)
Platform: x86_64-apple-darwin16.1.0 (64-bit)
Running under: macOS Sierra 10.12.3
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] GenomicAlignments_1.10.0 Rsamtools_1.26.1 Biostrings_2.42.1 XVector_0.14.0 SummarizedExperiment_1.4.0
[6] Biobase_2.34.0 GenomicRanges_1.26.2 GenomeInfoDb_1.10.3 IRanges_2.8.1 S4Vectors_0.12.1
[11] BiocGenerics_0.20.0
loaded via a namespace (and not attached):
[1] lattice_0.20-34 bitops_1.0-6 grid_3.3.2 zlibbioc_1.20.0 Matrix_1.2-8 BiocParallel_1.8.1 tools_3.3.2
[8] RCurl_1.95-4.8
Good to know. I misunderstand the meaning of GRangesList in this function. Thank you.