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Question: Report error in the stage of "Prepare the 'metadata' data frame" when running exomepeak() or metdiff with
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gravatar for 939930094
8 weeks ago by
9399300940
9399300940 wrote:

Hi everyone,

I'm using exomePeak to call m6A peaks with toy data and my MeRIP-Seq data, They both report the same error:

Import genomic features from the file as a GRanges object ... OK
Prepare the 'metadata' data frame ... Error in get(name, envir = asNamespace(pkg), inherits = FALSE) :
  找不到对象'.taxonomyId'

These are my commands, as described in "An Introduction to exomePeak":

> library("exomePeak")
> gtf <- system.file("extdata", "example.gtf", package="exomePeak")
> f1 <- system.file("extdata", "IP1.bam", package="exomePeak")
> f2 <- system.file("extdata", "IP2.bam", package="exomePeak")
> f3 <- system.file("extdata", "IP3.bam", package="exomePeak")
> f4 <- system.file("extdata", "IP4.bam", package="exomePeak")
> f5 <- system.file("extdata", "Input1.bam", package="exomePeak") 
> f6 <- system.file("extdata", "Input2.bam", package="exomePeak")
> f7 <- system.file("extdata", "Input3.bam", package="exomePeak")
> result <- exomepeak(GENE_ANNO_GTF=gtf,IP_BAM=c(f1,f2,f3,f4),INPUT_BAM=c(f5,f6,f7))

The sessionInfo() output:

sessionInfo()
R version 3.4.2 (2017-09-28)
Platform: x86_64-redhat-linux-gnu (64-bit)
Running under: CentOS Linux 7 (Core)

Matrix products: default
BLAS/LAPACK: /usr/lib64/R/lib/libRblas.so

locale:
 [1] LC_CTYPE=zh_CN.utf8       LC_NUMERIC=C             
 [3] LC_TIME=zh_CN.utf8        LC_COLLATE=zh_CN.utf8    
 [5] LC_MONETARY=zh_CN.utf8    LC_MESSAGES=zh_CN.utf8   
 [7] LC_PAPER=zh_CN.utf8       LC_NAME=C                
 [9] LC_ADDRESS=C              LC_TELEPHONE=C           
[11] LC_MEASUREMENT=zh_CN.utf8 LC_IDENTIFICATION=C      

attached base packages:
[1] stats4    parallel  stats     graphics  grDevices utils     datasets 
[8] methods   base     

other attached packages:
 [1] exomePeak_2.13.2           GenomicAlignments_1.14.2  
 [3] SummarizedExperiment_1.8.1 DelayedArray_0.4.1        
 [5] matrixStats_0.54.0         rtracklayer_1.38.3        
 [7] GenomicFeatures_1.30.3     AnnotationDbi_1.40.0      
 [9] Biobase_2.38.0             Rsamtools_1.30.0          
[11] Biostrings_2.46.0          XVector_0.18.0            
[13] GenomicRanges_1.30.3       GenomeInfoDb_1.16.0       
[15] IRanges_2.14.10            S4Vectors_0.19.19 
[17] BiocGenerics_0.26.0       

loaded via a namespace (and not attached):
 [1] Rcpp_0.12.18           compiler_3.4.2         prettyunits_1.0.2     
 [4] bitops_1.0-6           tools_3.4.2            zlibbioc_1.24.0       
 [7] progress_1.2.0         biomaRt_2.34.2         digest_0.6.17         
[10] bit_1.1-14             lattice_0.20-35        RSQLite_2.1.1         
[13] memoise_1.1.0          pkgconfig_2.0.2        rlang_0.2.2           
[16] Matrix_1.2-14          DBI_1.0.0              GenomeInfoDbData_1.0.0
[19] stringr_1.3.1          httr_1.3.1             hms_0.4.2             
[22] grid_3.4.2             bit64_0.9-7            R6_2.2.2              
[25] XML_3.98-1.16          RMySQL_0.10.15         BiocParallel_1.12.0   
[28] blob_1.1.1             magrittr_1.5           assertthat_0.2.0      
[31] stringi_1.2.4          RCurl_1.95-4.11        crayon_1.3.4

Here is the traceback:

6: get(name, envir = asNamespace(pkg), inherits = FALSE)
5: GenomeInfoDb:::.taxonomyId
4: .prepareGFFMetadata(file, dataSource, organism, taxonomyId, miRBaseBuild, 
       metadata)
3: makeTxDbFromGFF(PARAMETERS$GENE_ANNO_GTF, format = "gtf")
2: .read.gtf(PARAMETERS)
1: exomepeak(GENE_ANNO_GTF = gtf, IP_BAM = c(f1, f2, f3, f4), INPUT_BAM = c(f5, 
       f6, f7))

The same error also occured when using metdiff() with example data and commands. What's the problem and how can I fix it?  Thanks a lot!

 

 

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