champ.SVD() error, assumes standard class() function will return single string
0
0
Entering edit mode
@8df9ba1f
Last seen 12 days ago
Ireland

Enter the body of text here

Code should be placed in three backticks as shown below

I get the following error when running champ.SVD()

Error in if (class(beta) == "data.frame") { : │~ the condition has length > 1

and it cannot proceed. So beta's class is often a "matrix" "array" which is two strings, so the error seems report is evident. A check on the length of what class() returns would solve this. Seems to be a bit of an oversight.

r$> sessionInfo()
R version 4.2.0 (2022-04-22)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Debian GNU/Linux bookworm/sid

Matrix products: default
BLAS/LAPACK: /usr/lib/x86_64-linux-gnu/openblas-pthread/libopenblasp-r0.3.20.so

locale:
 [1] LC_CTYPE=en_IE.UTF-8       LC_NUMERIC=C               LC_TIME=en_IE.UTF-8        LC_COLLATE=en_IE.UTF-8
 [5] LC_MONETARY=en_IE.UTF-8    LC_MESSAGES=en_IE.UTF-8    LC_PAPER=en_IE.UTF-8       LC_NAME=C
 [9] LC_ADDRESS=C               LC_TELEPHONE=C             LC_MEASUREMENT=en_IE.UTF-8 LC_IDENTIFICATION=C

attached base packages:
[1] parallel  stats4    stats     graphics  grDevices utils     datasets  methods   base

other attached packages:
 [1] Cairo_1.5-15                               gplots_3.1.3                               pathfindR_1.6.3
 [4] pathfindR.data_1.1.2                       dplyr_1.0.9                                reshape_0.8.9
 [7] enrichplot_1.16.1                          clusterProfiler_4.4.1                      EnhancedVolcano_1.14.0
[10] ggrepel_0.9.1                              ggplot2_3.3.6                              limma_3.52.1
[13] sva_3.44.0                                 BiocParallel_1.30.2                        genefilter_1.78.0
[16] mgcv_1.8-40                                nlme_3.1-157                               RColorBrewer_1.1-3
[19] ChAMP_2.26.0                               RPMM_1.25                                  cluster_2.1.3
[22] DT_0.23                                    IlluminaHumanMethylationEPICmanifest_0.3.0 Illumina450ProbeVariants.db_1.32.0
[25] DMRcate_2.10.0                             ChAMPdata_2.28.0                           minfi_1.42.0
[28] bumphunter_1.38.0                          locfit_1.5-9.5                             iterators_1.0.14
[31] foreach_1.5.2                              Biostrings_2.64.0                          XVector_0.36.0
[34] SummarizedExperiment_1.26.1                Biobase_2.56.0                             MatrixGenerics_1.8.0
[37] matrixStats_0.62.0                         GenomicRanges_1.48.0                       GenomeInfoDb_1.32.2
[40] IRanges_2.30.0                             S4Vectors_0.34.0                           BiocGenerics_0.42.0

loaded via a namespace (and not attached):
  [1] Hmisc_4.7-0                                         Rsamtools_2.12.0
  [3] crayon_1.5.1                                        MASS_7.3-57
  [5] rhdf5filters_1.8.0                                  backports_1.4.1
  [7] impute_1.70.0                                       GOSemSim_2.22.0
  [9] rlang_1.0.2                                         DSS_2.44.0
 [11] filelock_1.0.2                                      rjson_0.2.21
 [13] globaltest_5.50.0                                   bit64_4.0.5
 [15] glue_1.6.2                                          isva_1.9
 [17] rngtools_1.5.2                                      methylumi_2.42.0
 [19] AnnotationDbi_1.58.0                                DOSE_3.22.0
 [21] tidyselect_1.1.2                                    XML_3.99-0.9
 [23] nleqslv_3.3.2                                       tidyr_1.2.0
 [25] GenomicAlignments_1.32.0                            xtable_1.8-4
 [27] magrittr_2.0.3                                      evaluate_0.15
 [29] cli_3.3.0                                           zlibbioc_1.42.0
 [31] rstudioapi_0.13                                     doRNG_1.8.2
 [33] rpart_4.1.16                                        fastmatch_1.1-3
 [35] ensembldb_2.20.1                                    treeio_1.20.0
 [37] IlluminaHumanMethylationEPICanno.ilm10b4.hg19_0.6.0 shiny_1.7.1
 [39] xfun_0.31                                           askpass_1.1
 [41] clue_0.3-60                                         multtest_2.52.0
 [43] caTools_1.18.2                                      tidygraph_1.2.1
 [45] KEGGREST_1.36.0                                     tibble_3.1.7
 [47] interactiveDisplayBase_1.34.0                       base64_2.0
 [49] ape_5.6-2                                           biovizBase_1.44.0
 [51] scrime_1.3.5                                        dendextend_1.15.2
 [53] png_0.1-7                                           permute_0.9-7
 [55] withr_2.5.0                                         lumi_2.48.0
 [57] bitops_1.0-7                                        ggforce_0.3.3
 [59] plyr_1.8.7                                          AnnotationFilter_1.20.0
 [61] JADE_2.0-3                                          pillar_1.7.0
 [63] cachem_1.0.6                                        GenomicFeatures_1.48.1
 [65] DelayedMatrixStats_1.18.0                           vctrs_0.4.1
 [67] ellipsis_0.3.2                                      generics_0.1.2
 [69] tools_4.2.0                                         foreign_0.8-82
 [71] munsell_0.5.0                                       tweenr_1.0.2
 [73] fgsea_1.22.0                                        DelayedArray_0.22.0
 [75] fastmap_1.1.0                                       compiler_4.2.0
 [77] httpuv_1.6.5                                        rtracklayer_1.56.0
 [79] geneLenDataBase_1.32.0                              ExperimentHub_2.4.0
 [81] beanplot_1.3.1                                      Gviz_1.40.1
 [83] plotly_4.10.0                                       GenomeInfoDbData_1.2.8
 [85] gridExtra_2.3                                       DNAcopy_1.70.0
 [87] edgeR_3.38.1                                        lattice_0.20-45
 [89] utf8_1.2.2                                          later_1.3.0
 [91] BiocFileCache_2.4.0                                 jsonlite_1.8.0
 [93] affy_1.74.0                                         scales_1.2.0
 [95] tidytree_0.3.9                                      sparseMatrixStats_1.8.0
 [97] lazyeval_0.2.2                                      promises_1.2.0.1
 [99] doParallel_1.0.17                                   latticeExtra_0.6-29
[101] R.utils_2.11.0                                      goseq_1.48.0
[103] checkmate_2.1.0                                     rmarkdown_2.14
[105] nor1mix_1.3-0                                       statmod_1.4.36
[107] siggenes_1.70.0                                     dichromat_2.0-0.1
[109] downloader_0.4                                      BSgenome_1.64.0
[111] igraph_1.3.1                                        HDF5Array_1.24.0
[113] bsseq_1.32.0                                        survival_3.3-1
[115] yaml_2.3.5                                          htmltools_0.5.2
[117] memoise_2.0.1                                       VariantAnnotation_1.42.1
[119] BiocIO_1.6.0                                        graphlayouts_0.8.0
[121] quadprog_1.5-8                                      viridisLite_0.4.0
[123] digest_0.6.29                                       assertthat_0.2.1
[125] mime_0.12                                           rappdirs_0.3.3
[127] BiasedUrn_1.07                                      RSQLite_2.2.14
[129] yulab.utils_0.0.4                                   data.table_1.14.2
[131] blob_1.2.3                                          R.oo_1.24.0
[133] preprocessCore_1.58.0                               fastICA_1.2-3
[135] shinythemes_1.2.0                                   splines_4.2.0
[137] Formula_1.2-4                                       Rhdf5lib_1.18.2
[139] illuminaio_0.38.0                                   AnnotationHub_3.4.0
[141] ProtGenerics_1.28.0                                 RCurl_1.98-1.6
[143] hms_1.1.1                                           rhdf5_2.40.0
[145] colorspace_2.0-3                                    base64enc_0.1-3
[147] BiocManager_1.30.17                                 aplot_0.1.4
[149] nnet_7.3-17                                         GEOquery_2.64.2
[151] Rcpp_1.0.8.3                                        mclust_5.4.9
[153] fansi_1.0.3                                         tzdb_0.3.0
[155] R6_2.5.1                                            grid_4.2.0
[157] lifecycle_1.0.1                                     curl_4.3.2
[159] kpmt_0.1.0                                          affyio_1.66.0
[161] DO.db_2.9                                           Matrix_1.4-1
[163] qvalue_2.28.0                                       ROC_1.72.0
[165] org.Hs.eg.db_3.15.0                                 stringr_1.4.0
[167] IlluminaHumanMethylation450kmanifest_0.4.0          htmlwidgets_1.5.4
[169] polyclip_1.10-0                                     biomaRt_2.52.0
[171] purrr_0.3.4                                         missMethyl_1.30.0
[173] shadowtext_0.1.2                                    gridGraphics_0.5-1
[175] marray_1.74.0                                       openssl_2.0.1
[177] htmlTable_2.4.0                                     patchwork_1.1.1
[179] codetools_0.2-18                                    IlluminaHumanMethylation450kanno.ilmn12.hg19_0.6.1
[181] GO.db_3.15.0                                        gtools_3.9.2
[183] prettyunits_1.1.1                                   dbplyr_2.1.1
[185] R.methodsS3_1.8.1                                   gtable_0.3.0
[187] DBI_1.1.2                                           wateRmelon_2.2.0
[189] ggfun_0.0.6                                         httr_1.4.3
[191] KernSmooth_2.23-20                                  stringi_1.7.6
[193] progress_1.2.2                                      reshape2_1.4.4
[195] farver_2.1.0                                        annotate_1.74.0
[197] viridis_0.6.2                                       ggtree_3.4.0
[199] xml2_1.3.3                                          combinat_0.0-8
[201] restfulr_0.0.13                                     readr_2.1.2
[203] ggplotify_0.1.0                                     BiocVersion_3.15.2
[205] bit_4.0.4                                           scatterpie_0.1.7
[207] jpeg_0.1-9                                          ggraph_2.0.5
[209] pkgconfig_2.0.3                                     knitr_1.39

r$>
ChAMP • 85 views
ADD COMMENT
0
Entering edit mode

What is class(yourbeta) ?

ADD REPLY

Login before adding your answer.

Traffic: 423 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6