[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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