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MLSC

2016-Sep-01 10:24 UTC

[R] Error while running Vegas function in cpvSNP package

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"> gs2GeneSetCollection
  names: NA (1 total)
  unique identifiers: 730005, 23755, ..., 23762 (8 total)
  types in collection:
    geneIdType: NullIdentifier (1 total)
    collectionType: NullCollection (1 total)> snpsGSCGeneSetCollection
  names: NA (1 total)
  unique identifiers: rs9608956, rs6518694, ..., rs2240176 (117 total)
  types in collection:
    geneIdType: AnnotationIdentifier (1 total)
    collectionType: NullCollection (1 total)> grGRanges 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

	[[alternative HTML version deleted]]

caitlin mchugh

2016-Sep-06 18:40 UTC

head link

[R] Error while running Vegas function in cpvSNP package

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
>
>
>

R help - Sep 2016 - Error while running Vegas function in cpvSNP package

[R] Error while running Vegas function in cpvSNP package

[R] Error while running Vegas function in cpvSNP package