Not able to Annotate CpG Island using methylKit
1
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Entering edit mode
@11d686c2
Last seen 22 days ago
India

Hi Team

I am evaluating my CpG island and annotating it. However, while doing the annotation I am getting the error. I also tried using example bed file shown in the methylKit documentation but the result is same.

        myDiff25p=getMethylDiff(myDiff,difference=25,qvalue=0.01)

        gene.obj=readTranscriptFeatures("C:/R-Data/Bismark_using/hgTables.bed.txt")    

        annotateWithGeneParts(as(myDiff25p,"GRanges"),gene.obj)

# please also include the results of running the following in an R session 
 > annotateWithGeneParts(as(myDiff25p.hyper,"GRanges"),gene.obj)
Warning in .Seqinfo.mergexy(x, y) :
  The 2 combined objects have no sequence levels in common. (Use
  suppressWarnings() to suppress this warning.)
Warning in .Seqinfo.mergexy(x, y) :
  The 2 combined objects have no sequence levels in common. (Use
  suppressWarnings() to suppress this warning.)
Warning in .Seqinfo.mergexy(x, y) :
  The 2 combined objects have no sequence levels in common. (Use
  suppressWarnings() to suppress this warning.)
Warning in .Seqinfo.mergexy(x, y) :
  The 2 combined objects have no sequence levels in common. (Use
  suppressWarnings() to suppress this warning.)
Warning in .Seqinfo.mergexy(x, y) :
  The 2 combined objects have no sequence levels in common. (Use
  suppressWarnings() to suppress this warning.)
Warning in .Seqinfo.mergexy(x, y) :
  The 2 combined objects have no sequence levels in common. (Use
  suppressWarnings() to suppress this warning.)
Error in h(simpleError(msg, call)) : 
  error in evaluating the argument 'x' in selecting a method for function 'nearest': error in evaluating the argument 'x' in selecting a method for function 'ranges': subscript contains NAs

## TraceBack

Error in h(simpleError(msg, call)) : error in evaluating the argument 'x' in selecting a method for function 'nearest': error in evaluating the argument 'x' in selecting a method for function 'ranges': subscript contains NAs
19.
h(simpleError(msg, call))
18.
.handleSimpleError(function (cond) .Internal(C_tryCatchHelper(addr, 1L, cond)), "error in evaluating the argument 'x' in selecting a method for function 'ranges': subscript contains NAs", base::quote(h(simpleError(msg, call))))
17.
h(simpleError(msg, call))
16.
.handleSimpleError(function (cond) .Internal(C_tryCatchHelper(addr, 1L, cond)), "subscript contains NAs", base::quote(NSBS(i, x, exact = exact, strict.upper.bound = !allow.append, allow.NAs = allow.NAs)))
15.
stop("subscript contains NAs")
14.
NSBS(i, x, exact = exact, strict.upper.bound = !allow.append, allow.NAs = allow.NAs)
13.
NSBS(i, x, exact = exact, strict.upper.bound = !allow.append, allow.NAs = allow.NAs)
12.
normalizeSingleBracketSubscript(i, x, as.NSBS = TRUE)
11.
extractROWS(x, i)
10.
extractROWS(x, i)
9.
subset_along_ROWS(x, i, drop = drop)
8.
g.bed[seqnames(g.bed) == chrs[i], ]
7.
g.bed[seqnames(g.bed) == chrs[i], ]
6.
ranges(g.bed[seqnames(g.bed) == chrs[i], ])
5.
nearest(ranges(g.bed[seqnames(g.bed) == chrs[i], ]), ranges(subject[seqnames(subject) == chrs[i], ]))
4.
.nearest.2bed(g.idh, tss)
3.
distance2NearestFeature(target, feature$TSSes)
2.
annotateWithGeneParts(as(myDiff25p.hyper_sub, "GRanges"), gene.obj)
1.
annotateWithGeneParts(as(myDiff25p.hyper_sub, "GRanges"), gene.obj)


sessionInfo( )

R version 4.1.1 (2021-08-10)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 10 x64 (build 19043)

Matrix products: default

locale:
[1] LC_COLLATE=English_India.1252  LC_CTYPE=English_India.1252   
[3] LC_MONETARY=English_India.1252 LC_NUMERIC=C                  
[5] LC_TIME=English_India.1252    

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

other attached packages:
 [1] genomation_1.24.0           DSS_2.40.0                  bsseq_1.28.0               
 [4] SummarizedExperiment_1.22.0 MatrixGenerics_1.4.3        matrixStats_0.60.1         
 [7] BiocParallel_1.26.2         Biobase_2.52.0              methylKit_1.18.0           
[10] GenomicRanges_1.44.0        GenomeInfoDb_1.28.4         IRanges_2.26.0             
[13] S4Vectors_0.30.0            BiocGenerics_0.38.0        

loaded via a namespace (and not attached):
 [1] nlme_3.1-153              bitops_1.0-7              bit64_4.0.5              
 [4] numDeriv_2016.8-1.1       tools_4.1.1               utf8_1.2.2               
 [7] R6_2.5.1                  KernSmooth_2.23-20        HDF5Array_1.20.0         
[10] mgcv_1.8-36               DBI_1.1.1                 colorspace_2.0-2         
[13] seqPattern_1.24.0         permute_0.9-5             rhdf5filters_1.4.0       
[16] fastseg_1.38.0            tidyselect_1.1.1          bit_4.0.4                
[19] compiler_4.1.1            cli_3.0.1                 DelayedArray_0.18.0      
[22] rtracklayer_1.52.1        scales_1.1.1              mvtnorm_1.1-2            
[25] readr_2.0.1               stringr_1.4.0             digest_0.6.27            
[28] Rsamtools_2.8.0           rmarkdown_2.11            R.utils_2.10.1           
[31] XVector_0.32.0            pkgconfig_2.0.3           htmltools_0.5.2          
[34] plotrix_3.8-2             sparseMatrixStats_1.4.2   fastmap_1.1.0            
[37] bbmle_1.0.24              limma_3.48.3              BSgenome_1.60.0          
[40] rlang_0.4.11              impute_1.66.0             rstudioapi_0.13          
[43] DelayedMatrixStats_1.14.3 BiocIO_1.2.0              generics_0.1.0           
[46] vroom_1.5.5               mclust_5.4.7              gtools_3.9.2             
[49] dplyr_1.0.7               R.oo_1.24.0               RCurl_1.98-1.5           
[52] magrittr_2.0.1            GenomeInfoDbData_1.2.6    Matrix_1.3-4             
[55] Rcpp_1.0.7                munsell_0.5.0             Rhdf5lib_1.14.2          
[58] fansi_0.5.0               lifecycle_1.0.0           R.methodsS3_1.8.1        
[61] stringi_1.7.4             yaml_2.2.1                MASS_7.3-54              
[64] zlibbioc_1.38.0           rhdf5_2.36.0              plyr_1.8.6               
[67] qvalue_2.24.0             bdsmatrix_1.3-4           crayon_1.4.1             
[70] lattice_0.20-44           Biostrings_2.60.2         splines_4.1.1            
[73] hms_1.1.0                 locfit_1.5-9.4            knitr_1.34               
[76] pillar_1.6.2              rjson_0.2.20              reshape2_1.4.4           
[79] XML_3.99-0.8              glue_1.4.2                evaluate_0.14            
[82] data.table_1.14.0         tzdb_0.1.2                vctrs_0.3.8              
[85] gtable_0.3.0              purrr_0.3.4               assertthat_0.2.1         
[88] ggplot2_3.3.5             emdbook_1.3.12            gridBase_0.4-7           
[91] xfun_0.26                 restfulr_0.0.13           coda_0.19-4              
[94] tibble_3.1.4              GenomicAlignments_1.28.0  ellipsis_0.3.2
annotateWithGeneParts methylKit • 100 views
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1
Entering edit mode
@11d686c2
Last seen 22 days ago
India

Hi

I resolved the problem. The error was coming because of Chromosome numbering. Bed files was having "Chr" which i removed and resolved the problem.

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