Entering edit mode
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
