[R] Error while running Vegas function in cpvSNP package
caitlin mchugh
c8linmch at googlemail.com
Tue Sep 6 20:40:28 CEST 2016
Hello,
Please find attached a script where I tried to replicate the issue. I was
unable to reproduce the error. Perhaps you can send me more details?
Also, it appears the LD matrix you are using is not symmetric nor does it
have 1's on the diagonal. Both of these things should be satisfied for the
algorithm to work properly.
Feel free to let me know if you continue to run into errors.
Thanks,
Caitlin
On Thu, Sep 1, 2016 at 6:24 AM, MLSC <mlscmahe at gmail.com> wrote:
> Hello Sir,
>
> When I try to run vegas() function, I come across below errors, can
> somebody help me in fixing this issue?
>
> > test<-vegas(snpsGSC, gr,ldMat,1000,correction=TRUE,seed=NULL,
> verbose=FALSE)
> Warning: coercing ldMatrix from data.frame to matrix.
> Error in validObject(.Object) :
> invalid class “VEGASResultCollection” object: members must all be
> 'VEGASResult' classes
> > test<-vegas(gs2, gr,ldMat,1000,correction=TRUE,seed=NULL, verbose=FALSE)
> Warning: coercing ldMatrix from data.frame to matrix.
> Error in validObject(.Object) :
> invalid class “VEGASResultCollection” object: members must all be
> 'VEGASResult' classes
>
>
> Please find structure of objects used inside vegas(), below
>
>
> > class(gs2)
> [1] "GeneSetCollection"
> attr(,"package")
> [1] "GSEABase"
> > gs2
> GeneSetCollection
> names: NA (1 total)
> unique identifiers: 730005, 23755, ..., 23762 (8 total)
> types in collection:
> geneIdType: NullIdentifier (1 total)
> collectionType: NullCollection (1 total)
> > snpsGSC
> GeneSetCollection
> names: NA (1 total)
> unique identifiers: rs9608956, rs6518694, ..., rs2240176 (117 total)
> types in collection:
> geneIdType: AnnotationIdentifier (1 total)
> collectionType: NullCollection (1 total)
> > gr
> GRanges object with 10357 ranges and 6 metadata columns:
> seqnames ranges strand | P SNP
> <Rle> <IRanges> <Rle> | <numeric> <character>
> [1] chr22 [16114244, 16114244] * | 0.9298 rs12157537
> [2] chr22 [16494187, 16494187] * | 0.2571 rs8142331
> [3] chr22 [16855618, 16855618] * | 0.3743 rs5747010
> [4] chr22 [17012935, 17012935] * | 0.1005 rs9604821
> [5] chr22 [17057138, 17057138] * | 0.5120 rs5746647
> ... ... ... ... ... ... ...
> [10353] chr22 [51171693, 51171693] * | 0.6500 rs756638
> [10354] chr22 [51175626, 51175626] * | 0.5235 rs3810648
> [10355] chr22 [51178090, 51178090] * | 0.2008 rs2285395
> [10356] chr22 [51181759, 51181759] * | 0.4858 rs13056621
> [10357] chr22 [51211392, 51211392] * | 0.2952 rs3888396
> Position Chromosome Start End
> <integer> <factor> <integer> <integer>
> [1] 16114244 chr22 16114244 16114244
> [2] 16494187 chr22 16494187 16494187
> [3] 16855618 chr22 16855618 16855618
> [4] 17012935 chr22 17012935 17012935
> [5] 17057138 chr22 17057138 17057138
> ... ... ... ... ...
> [10353] 51171693 chr22 51171693 51171693
> [10354] 51175626 chr22 51175626 51175626
> [10355] 51178090 chr22 51178090 51178090
> [10356] 51181759 chr22 51181759 51181759
> [10357] 51211392 chr22 51211392 51211392
> -------
> seqinfo: 1 sequence from an unspecified genome; no seqlengths
>
> >ldMat
> rs756638 rs3810648 rs2285395 rs13056621 rs3888396
> rs133433 2.302381e-04 1.593234e-03 1.745740e-03 3.279513e-03 1.135283e-03
> rs4645824 3.435556e-04 2.872766e-03 6.350416e-05 9.143595e-04 2.032939e-03
> rs12165592 1.164639e-04 6.331347e-03 1.911289e-03 2.124385e-03 7.972265e-04
> rs2413348 1.148297e-04 4.106582e-03 1.857187e-03 9.805785e-04 5.707284e-04
> rs5755729 6.863351e-04 7.718787e-04 1.794326e-04 9.102677e-05 1.835078e-05
> rs5755730 6.606449e-04 1.817608e-03 2.795217e-04 2.912946e-04 1.582141e-03
> rs738207 3.193647e-03 1.833686e-06 2.162108e-06 1.377696e-03 3.024123e-03
> rs28528068 5.097169e-04 9.289022e-05 8.253080e-05 9.775527e-06 4.618146e-04
> rs9610304 2.185120e-05 1.753900e-03 3.760546e-04 4.235130e-06 7.791331e-04
> rs5999844 1.511305e-04 5.263161e-05 1.594619e-04 3.668878e-04 9.886630e-05
> rs8136332 1.466643e-04 6.929900e-04 1.128017e-05 1.327246e-03 3.758860e-04
> rs909704 9.107431e-05 6.988505e-05 8.734125e-04 6.070963e-04 1.666259e-05
> rs10483191 1.563958e-04 6.843857e-04 1.050799e-05 1.289273e-03 3.944796e-04
> rs880211 7.008708e-05 3.167541e-03 6.418652e-04 2.483367e-04 1.344723e-03
> rs1107498 1.888331e-04 2.733062e-03 6.233536e-04 3.931746e-04 1.341147e-03
> rs5999855 3.143964e-05 5.473455e-03 1.166912e-03 4.374772e-03 2.152193e-03
> rs9610308 1.579521e-05 5.385714e-06 1.199517e-06 3.337275e-03 4.705493e-04
> rs713968 1.125728e-03 2.431651e-05 7.292905e-05 9.684127e-04 6.402607e-05
> rs139059 2.946244e-04 2.765441e-04 2.785183e-06 7.474786e-04 3.190005e-04
> [ reached getOption("max.print") -- omitted 4981 rows ]
>
> Please find session info below,
> > sessionInfo()
> R version 3.2.4 Revised (2016-03-16 r70336)
> Platform: x86_64-pc-linux-gnu/64 (64-bit)
>
> 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] TxDb.Hsapiens.UCSC.hg18.knownGene_3.2.2
> [2] VariantAnnotation_1.16.4
> [3] Rsamtools_1.22.0
> [4] Biostrings_2.38.4
> [5] XVector_0.10.0
> [6] SummarizedExperiment_1.0.2
> [7] biomaRt_2.26.1
> [8] snpStats_1.20.0
> [9] Matrix_1.2-6
> [10] survival_2.39-5
> [11] genetics_1.3.8.1
> [12] mvtnorm_1.0-5
> [13] gtools_3.5.0
> [14] gdata_2.17.0
> [15] combinat_0.0-8
> [16] MultiPhen_2.0.1
> [17] meta_4.5-0
> [18] epitools_0.5-7
> [19] abind_1.4-5
> [20] MASS_7.3-45
> [21] BiocInstaller_1.20.3
> [22] TxDb.Hsapiens.UCSC.hg19.knownGene_3.2.2
> [23] cpvSNP_1.2.0
> [24] GSEABase_1.32.0
> [25] graph_1.48.0
> [26] annotate_1.48.0
> [27] XML_3.98-1.4
> [28] GenomicFeatures_1.22.13
> [29] AnnotationDbi_1.32.3
> [30] Biobase_2.30.0
> [31] GenomicRanges_1.22.4
> [32] GenomeInfoDb_1.6.3
> [33] IRanges_2.4.8
> [34] S4Vectors_0.8.11
> [35] BiocGenerics_0.16.1
>
> loaded via a namespace (and not attached):
> [1] splines_3.2.4 lattice_0.20-33
> colorspace_1.2-6
> [4] rtracklayer_1.30.4 HardyWeinberg_1.5.6
> DBI_0.5
> [7] BiocParallel_1.4.3 RColorBrewer_1.1-2
> lambda.r_1.1.9
> [10] plyr_1.8.4 zlibbioc_1.16.0
> munsell_0.4.3
> [13] gtable_0.2.0 futile.logger_1.4.3
> caTools_1.17.1
> [16] Rcpp_0.12.6 KernSmooth_2.23-15
> xtable_1.8-2
> [19] corpcor_1.6.8 BSgenome_1.38.0
> scales_0.4.0
> [22] gplots_3.0.1 ggplot2_2.1.0
> grid_3.2.4
> [25] tools_3.2.4 bitops_1.0-6
> RCurl_1.95-4.8
> [28] RSQLite_1.0.0 mice_2.25
> futile.options_1.0.0
> [31] rpart_4.1-10 GenomicAlignments_1.6.3
> nnet_7.3-12
> >
>
> Thanking you in anticipation.
>
> Regards,
> Prashantha
>
>
>
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