calculateRPKM error in customProDB
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0
Entering edit mode
javamng ▴ 10
@javamng-13627
Last seen 4.5 years ago

I recently installed the customProDB package.

And when I run calculateRPKM, I get the following message

Please let me know if you have seen any of these problems.

thanks!

> sessionInfo()
R version 3.4.1 (2017-06-30)
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=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] stats4    parallel  stats     graphics  grDevices utils     datasets
[8] methods   base

other attached packages:
[1] customProDB_1.16.0   biomaRt_2.32.1       AnnotationDbi_1.38.2
[4] Biobase_2.36.2       IRanges_2.10.2       S4Vectors_0.14.3
[7] BiocGenerics_0.22.0

loaded via a namespace (and not attached):
 [1] Rcpp_0.12.12               plyr_1.8.4
 [3] compiler_3.4.1             GenomeInfoDb_1.12.2
 [5] XVector_0.16.0             GenomicFeatures_1.28.4
 [7] bitops_1.0-6               tools_3.4.1
 [9] zlibbioc_1.22.0            digest_0.6.12
[11] bit_1.1-12                 AhoCorasickTrie_0.1.0
[13] RSQLite_2.0                memoise_1.1.0
[15] tibble_1.3.3               lattice_0.20-35
[17] BSgenome_1.44.0            rlang_0.1.1
[19] Matrix_1.2-10              DelayedArray_0.2.7
[21] DBI_0.7                    GenomeInfoDbData_0.99.0
[23] stringr_1.2.0              rtracklayer_1.36.4
[25] Biostrings_2.44.2          bit64_0.9-7
[27] grid_3.4.1                 XML_3.98-1.9
[29] BiocParallel_1.10.1        magrittr_1.5
[31] blob_1.1.0                 Rsamtools_1.28.0
[33] matrixStats_0.52.2         GenomicRanges_1.28.4
[35] GenomicAlignments_1.12.1   SummarizedExperiment_1.6.3
[37] stringi_1.1.5              RCurl_1.95-4.8
[39] VariantAnnotation_1.22.3

--------- Error Messages -------

> RPKM <- calculateRPKM(bamFile, exon, proteincodingonly=TRUE, ids)
Error in keepSeqlevels(anno, seqlevels(galn)) :
  invalid seqlevels: KI270729.1, KI270743.1, GL000008.2, KI270747.1,
  KI270722.1, KI270742.1, KI270736.1, GL000224.1, KI270719.1, KI270712.1,
  KI270706.1, KI270725.1, KI270715.1, KI270749.1, KI270741.1, GL000221.1,
  KI270716.1, KI270751.1, KI270519.1, GL000214.1, KI270708.1, KI270730.1,
  KI270438.1, KI270737.1, KI270738.1, KI270748.1, KI270435.1, GL000208.1,
  KI270538.1, KI270756.1, KI270739.1, KI270757.1, KI270709.1, KI270746.1,
  KI270753.1, KI270589.1, KI270735.1, KI270745.1, KI270714.1, KI270732.1,
  KI270754.1, KI270710.1, KI270717.1, KI270724.1, KI270720.1, KI270723.1,
  KI270718.1, KI270317.1, KI270740.1, KI270755.1, KI270707.1, KI270579.1,
  KI270752.1, KI270512.1, KI270322.1, GL000226.1, KI270311.1, KI270366.1,
  KI270511.1, KI270448.1, KI270521.1, KI270581.1, KI270582.1, KI270515.1,
  KI270588.1, KI270591.1, KI270522.1, KI270507.1, KI270590.1, KI270584.1,
  KI270320.1, KI270382.1, KI270468.1, KI270467.1, KI270362.1, KI270517.1,
  KI270593.1, KI270528.1, KI270587.

 

software error customprodb • 1.0k views
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Entering edit mode
@georgesbedran-11010
Last seen 3.8 years ago

Hello,

since the last few bioconductor updates the keepSeqlevels functions had the default pruning.mode option changed to raise an erorr in case arg1 and arg2 contain different levels (chromosomes).

You only have to add the argument pruning.mode="coarse" to replicate the old behaviour.

You just have to replace lines 49 and 50 of the calcuteRPKM.R source code file with the following :

            anno <- keepSeqlevels(anno,seqlevels(galn), pruning.mode="coarse")
            galn <- keepSeqlevels(galn,seqlevels(anno), pruning.mode="coarse")

then add the whole modified function "calculateRPKM" to your script before calling it.

 

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Entering edit mode

Hello,

I am experiencing the same problem

> anno <- keepSeqlevels(anno, seqlevels(galn))
Error in keepSeqlevels(anno, seqlevels(galn)) : 
  invalid seqlevels: JH584301.1, JH584300.1, JH584302.1, GL456379.1, GL456393.1, GL456366.1, GL456367.1, GL456213.1,
  GL456383.1, GL456360.1, GL456378.1, GL456389.1, GL456370.1, GL456387.1, GL456390.1, GL456394.1, GL456392.1, GL456382.1,
  GL456359.1, GL456396.1, GL456368.1

Even with your suggestion it is still giving an error

> anno <- keepSeqlevels(anno,seqlevels(galn), pruning.mode="coarse")
Error in keepSeqlevels(anno, seqlevels(galn), pruning.mode = "coarse") : 
  invalid seqlevels: JH584301.1, JH584300.1, JH584302.1, GL456379.1, GL456393.1, GL456366.1, GL456367.1, GL456213.1,
  GL456383.1, GL456360.1, GL456378.1, GL456389.1, GL456370.1, GL456387.1, GL456390.1, GL456394.1, GL456392.1, GL456382.1,
  GL456359.1, GL456396.1, GL456368.1

 

Any idea how to fix this?

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Entering edit mode

I did as you prescribed but it did not fix the error.

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