[R] Error while running Vegas function in cpvSNP package

MLSC mlscmahe at gmail.com
Thu Sep 1 12:24:26 CEST 2016


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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