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Question: overlapPermTest will not allow randomizing from MASKED hg19
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gravatar for peds09
10 weeks ago by
peds090
peds090 wrote:

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  

ADD COMMENTlink written 10 weeks ago by peds090
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