Entering edit mode
When running DMP.GUI certain genes will display properly but others give me this error:
Error: arguments imply differing number of rows: 0, 1
Code:
DMP.GUI(DMP = myDMP[[1]], beta = M_values, pheno = Pheno$group_name)
preview of M_values:
TCGA.BF.A1PU.01 TCGA.BF.A1PV.01 TCGA.BF.A1PX.01 TCGA.BF.A1PZ.01
cg00000029 -3.514996212 -0.210358867 0.172034591 -1.827219305
cg00000165 -2.439962607 3.927620591 -0.166522368 1.773942073
preview of Pheno:
Sample_Name group_name
TCGA.BF.A1PU.01 C250T
TCGA.BF.A1PV.01 C228T
myDMP:
logFC AveExpr t P.Value adj.P.Val B mut_AVG WT_AVG deltaBeta CHR MAPINFO StrandType gene feature cgi feat.cgi UCSC_CpG_Islands_Name DHS Enhancer Phantom Probe_SNPs Probe_SNPs_10
cg21385983 0.892828713 -0.458177706 6.070326103 1.69E-08 0.00054363 9.069279849 -0.776490552 0.116338161 0.892828713 22 37215619 R II PVALB TSS200 shelf TSS200-shelf chr22:37212769-37213467 NA NA
cg13927088 1.081765896 1.260059068 3.635407474 0.000416778 0.016697866 -0.104369885 0.874386009 1.956151905 1.081765896 1 152691125 R II C1orf68 TSS1500 opensea TSS1500-opensea NA NA
When using the the gene in the first row (PVALB) with DMP.GUI the graph works, but when using the gene in the second row (C1orf68) I get the error: arguments imply differing number of rows: 0, 1
Any help would be greatly appreciated!
sessioninfo()
R version 4.2.0 (2022-04-22 ucrt)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 10 x64 (build 19042)
Matrix products: default
locale:
[1] LC_COLLATE=English_United States.utf8 LC_CTYPE=English_United States.utf8 LC_MONETARY=English_United States.utf8 LC_NUMERIC=C LC_TIME=English_United States.utf8
attached base packages:
[1] parallel stats4 stats graphics grDevices utils datasets methods base
other attached packages:
[1] shiny_1.7.1 dplyr_1.0.9 EnhancedVolcano_1.14.0
[4] ggrepel_0.9.1 ggplot2_3.3.6 IlluminaHumanMethylation450kmanifest_0.4.0
[7] IlluminaHumanMethylation450kanno.ilmn12.hg19_0.6.1 lumi_2.48.0 data.table_1.14.2
[10] ChAMP_2.26.0 RPMM_1.25 cluster_2.1.3
[13] DT_0.23 IlluminaHumanMethylationEPICmanifest_0.3.0 Illumina450ProbeVariants.db_1.32.0
[16] DMRcate_2.10.0 ChAMPdata_2.28.0 minfi_1.42.0
[19] bumphunter_1.38.0 locfit_1.5-9.5 iterators_1.0.14
[22] foreach_1.5.2 Biostrings_2.64.0 XVector_0.36.0
[25] SummarizedExperiment_1.26.1 Biobase_2.56.0 MatrixGenerics_1.8.0
[28] matrixStats_0.62.0 GenomicRanges_1.48.0 GenomeInfoDb_1.32.2
[31] IRanges_2.30.0 S4Vectors_0.34.0 BiocGenerics_0.42.0
loaded via a namespace (and not attached):
[1] rappdirs_0.3.3 rtracklayer_1.56.0 R.methodsS3_1.8.2
[4] wateRmelon_2.2.0 tidyr_1.2.0 bit64_4.0.5
[7] knitr_1.39 DelayedArray_0.22.0 R.utils_2.12.0
[10] rpart_4.1.16 KEGGREST_1.36.2 RCurl_1.98-1.7
[13] GEOquery_2.64.2 AnnotationFilter_1.20.0 doParallel_1.0.17
[16] generics_0.1.2 GenomicFeatures_1.48.3 preprocessCore_1.58.0
[19] RSQLite_2.2.14 combinat_0.0-8 bit_4.0.4
[22] tzdb_0.3.0 xml2_1.3.3 httpuv_1.6.5
[25] assertthat_0.2.1 viridis_0.6.2 IlluminaHumanMethylationEPICanno.ilm10b4.hg19_0.6.0
[28] isva_1.9 xfun_0.31 jquerylib_0.1.4
[31] hms_1.1.1 evaluate_0.15 missMethyl_1.30.0
[34] DNAcopy_1.70.0 promises_1.2.0.1 fansi_1.0.3
[37] restfulr_0.0.15 scrime_1.3.5 progress_1.2.2
[40] dendextend_1.15.2 dbplyr_2.2.1 DBI_1.1.3
[43] htmlwidgets_1.5.4 reshape_0.8.9 purrr_0.3.4
[46] ROC_1.72.0 ellipsis_0.3.2 crosstalk_1.2.0
[49] backports_1.4.1 permute_0.9-7 annotate_1.74.0
[52] biomaRt_2.52.0 sparseMatrixStats_1.8.0 vctrs_0.4.1
[55] ensembldb_2.20.2 withr_2.5.0 cachem_1.0.6
[58] globaltest_5.50.0 Gviz_1.40.1 BSgenome_1.64.0
[61] checkmate_2.1.0 GenomicAlignments_1.32.0 prettyunits_1.1.1
[64] mclust_5.4.10 ExperimentHub_2.4.0 lazyeval_0.2.2
[67] crayon_1.5.1 genefilter_1.78.0 edgeR_3.38.1
[70] pkgconfig_2.0.3 nlme_3.1-158 ProtGenerics_1.28.0
[73] nnet_7.3-17 rlang_1.0.2 lifecycle_1.0.1
[76] nleqslv_3.3.2 filelock_1.0.2 affyio_1.66.0
[79] BiocFileCache_2.4.0 AnnotationHub_3.4.0 dichromat_2.0-0.1
[82] rngtools_1.5.2 base64_2.0 Matrix_1.4-1
[85] Rhdf5lib_1.18.2 base64enc_0.1-3 geneLenDataBase_1.32.0
[88] viridisLite_0.4.0 png_0.1-7 rjson_0.2.21
[91] bitops_1.0-7 R.oo_1.25.0 KernSmooth_2.23-20
[94] rhdf5filters_1.8.0 blob_1.2.3 DelayedMatrixStats_1.18.0
[97] doRNG_1.8.2 stringr_1.4.0 qvalue_2.28.0
[100] nor1mix_1.3-0 readr_2.1.2 jpeg_0.1-9
[103] scales_1.2.0 memoise_2.0.1 magrittr_2.0.3
[106] plyr_1.8.7 zlibbioc_1.42.0 compiler_4.2.0
[109] BiocIO_1.6.0 RColorBrewer_1.1-3 illuminaio_0.38.0
[112] clue_0.3-61 Rsamtools_2.12.0 cli_3.3.0
[115] DSS_2.44.0 affy_1.74.0 JADE_2.0-3
[118] htmlTable_2.4.0 Formula_1.2-4 MASS_7.3-57
[121] mgcv_1.8-40 tidyselect_1.1.2 stringi_1.7.6
[124] yaml_2.3.5 askpass_1.1 latticeExtra_0.6-29
[127] grid_4.2.0 sass_0.4.1 VariantAnnotation_1.42.1
[130] tools_4.2.0 rstudioapi_0.13 foreign_0.8-82
[133] bsseq_1.32.0 gridExtra_2.3 farver_2.1.0
[136] digest_0.6.29 BiocManager_1.30.18 quadprog_1.5-8
[139] Rcpp_1.0.8.3 siggenes_1.70.0 BiocVersion_3.15.2
[142] later_1.3.0 org.Hs.eg.db_3.15.0 httr_1.4.3
[145] AnnotationDbi_1.58.0 biovizBase_1.44.0 colorspace_2.0-3
[148] XML_3.99-0.10 splines_4.2.0 statmod_1.4.36
[151] kpmt_0.1.0 multtest_2.52.0 shinythemes_1.2.0
[154] plotly_4.10.0 xtable_1.8-4 jsonlite_1.8.0
[157] marray_1.74.0 R6_2.5.1 Hmisc_4.7-0
[160] pillar_1.7.0 htmltools_0.5.2 mime_0.12
[163] glue_1.6.2 fastmap_1.1.0 BiocParallel_1.30.3
[166] interactiveDisplayBase_1.34.0 beanplot_1.3.1 codetools_0.2-18
[169] utf8_1.2.2 bslib_0.3.1 lattice_0.20-45
[172] tibble_3.1.7 sva_3.44.0 BiasedUrn_1.07
[175] curl_4.3.2 gtools_3.9.2.2 GO.db_3.15.0
[178] openssl_2.0.2 survival_3.3-1 limma_3.52.2
[181] rmarkdown_2.14 methylumi_2.42.0 fastICA_1.2-3
[184] munsell_0.5.0 rhdf5_2.40.0 GenomeInfoDbData_1.2.8
[187] goseq_1.48.0 impute_1.70.0 HDF5Array_1.24.1
[190] reshape2_1.4.4 gtable_0.3.0
