Using overlapPermTest to compare two GRanges objects - a and b. a is a ChIP seq broad peaks GEO dataset downloaded directly from Annotation Hub in Bioconductor. b is a GRanges list of widths of peaks of my own ChIP seq data. I tried the following code and it worked
random_list = overlapPermTest(a, b, ntimes=1000, genome="BSgenome.Hsapiens.UCSC.hg19", count.once=TRUE)
giving expected output as listed in regioneR tutorial.
But when I try to do the randomization on MASKED hg19 genome - which I downloaded here:
biocLite("BSgenome.Hsapiens.UCSC.hg19.masked")
library(BSgenome.Hsapiens.UCSC.hg19.masked)And I run the following:
random_list = overlapPermTest(a, b, ntimes=1000, genome="BSgenome.Hsapiens.UCSC.hg19.masked", count.once=TRUE)
It stalled x 3. No error message, just stopped computing and crashed my R session.
Any suggestions appreciated,
Thank you in advance,
Joy
# Session info:
R version 3.4.4 (2018-03-15)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 18.04 LTS
Matrix products: default
BLAS: /usr/lib/x86_64-linux-gnu/blas/libblas.so.3.7.1
LAPACK: /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.7.1
locale:
[1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C
[3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8
[5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8
[7] LC_PAPER=en_US.UTF-8 LC_NAME=C
[9] LC_ADDRESS=C LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
attached base packages:
[1] parallel stats4 stats graphics grDevices utils
[7] datasets methods base
other attached packages:
[1] yeastCC_1.18.0
[2] shiny_1.1.0
[3] SummarizedExperiment_1.8.1
[4] DelayedArray_0.4.1
[5] matrixStats_0.53.1
[6] Biobase_2.38.0
[7] BSgenome.Hsapiens.UCSC.hg19_1.4.0
[8] AnnotationHub_2.10.1
[9] regioneR_1.10.0
[10] BSgenome_1.46.0
[11] Biostrings_2.46.0
[12] XVector_0.18.0
[13] memoise_1.1.0
[14] rtracklayer_1.38.3
[15] GenomicRanges_1.30.3
[16] GenomeInfoDb_1.14.0
[17] IRanges_2.12.0
[18] S4Vectors_0.16.0
[19] BiocGenerics_0.24.0
[20] BiocInstaller_1.28.0
loaded via a namespace (and not attached):
[1] Rcpp_0.12.17 later_0.7.3
[3] compiler_3.4.4 bitops_1.0-6
[5] tools_3.4.4 zlibbioc_1.24.0
[7] digest_0.6.15 bit_1.1-14
[9] jsonlite_1.5 RSQLite_2.1.1
[11] lattice_0.20-35 rlang_0.2.1
[13] pkgconfig_2.0.1 Matrix_1.2-12
[15] DBI_1.0.0 curl_3.2
[17] yaml_2.1.19 GenomeInfoDbData_1.0.0
[19] httr_1.3.1 bit64_0.9-7
[21] grid_3.4.4 R6_2.2.2
[23] AnnotationDbi_1.40.0 XML_3.98-1.11
[25] BiocParallel_1.12.0 magrittr_1.5
[27] blob_1.1.1 promises_1.0.1
[29] htmltools_0.3.6 Rsamtools_1.30.0
[31] GenomicAlignments_ 1.14.2 xtable_1.8-2
[33] mime_0.5 interactiveDisplayBase_1.16.0
[35] httpuv_1.4.4.2 RCurl_1.95-4.10
