Entering edit mode
Hi all,
I'm trying to get ELMER running on some of my own EPIC/RNAseq data but first I need to get the example working.
I'm encountering an error simply following the example, am I missing packages? (sessioninfo below):
> library(ELMER)
> # example input
> met <- matrix(rep(0,15),ncol = 5)
> colnames(met) <- c("Sample1",
+ "Sample2",
+ "Sample3",
+ "Sample4",
+ "Sample5")
> rownames(met) <- c("cg26928153","cg16269199","cg13869341")
>
> exp <- matrix(rep(0,15),ncol = 5)
> colnames(exp) <- c("Sample1",
+ "Sample2",
+ "Sample3",
+ "Sample4",
+ "Sample5")
> rownames(exp) <- c("ENSG00000073282","ENSG00000078900","ENSG00000141510")
>
>
> assay <- c(rep("DNA methylation", ncol(met)),
+ rep("Gene expression", ncol(exp)))
> primary <- c(colnames(met),colnames(exp))
> colname <- c(colnames(met),colnames(exp))
> sampleMap <- data.frame(assay,primary,colname)
>
> distal.probes <- get.feature.probe(genome = "hg19",
+ met.platform = "EPIC")
Accessing grch37.ensembl.org to get TSS information
Downloading transcripts information from http://grch37.ensembl.org:80/biomart/martservice. Using: Human genes (GRCh37.p13)
Loading from disk
Returning distal probes: 341894
>
> colData <- data.frame(sample = colnames(met))
> rownames(colData) <- colnames(met)
>
> mae <- createMAE(exp = exp,
+ met = met,
+ save = TRUE,
+ filter.probes = distal.probes,
+ colData = colData,
+ sampleMap = sampleMap,
+ linearize.exp = TRUE,
+ save.filename = "mae.rda",
+ met.platform = "EPIC",
+ genome = "hg19",
+ TCGA = FALSE)
=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-
Creating a SummarizedExperiment from gene expression input
Accessing grch37.ensembl.org to get gene information
Downloading genome information (try:0) Using: Human genes (GRCh37.p13)
Error: $ operator is invalid for atomic vectors
Any suggestions appreciated!
Cheers,
Dean
> sessionInfo()
R version 3.6.0 (2019-04-26)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 16.04.6 LTS
Matrix products: default
BLAS: /usr/lib/libblas/libblas.so.3.6.0
LAPACK: /usr/lib/lapack/liblapack.so.3.6.0
locale:
[1] LC_CTYPE=en_GB.UTF-8 LC_NUMERIC=C LC_TIME=en_GB.UTF-8 LC_COLLATE=en_GB.UTF-8 LC_MONETARY=en_GB.UTF-8
[6] LC_MESSAGES=en_GB.UTF-8 LC_PAPER=en_GB.UTF-8 LC_NAME=C LC_ADDRESS=C LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_GB.UTF-8 LC_IDENTIFICATION=C
attached base packages:
[1] parallel stats4 stats graphics grDevices utils datasets methods base
other attached packages:
[1] biomaRt_2.40.1 sva_3.32.1 genefilter_1.66.0 mgcv_1.8-28 nlme_3.1-139
[6] edgeR_3.26.5 limma_3.40.2 ELMER_2.8.0 ELMER.data_2.8.0 MultiAssayExperiment_1.10.4
[11] SummarizedExperiment_1.14.0 DelayedArray_0.10.0 BiocParallel_1.18.0 matrixStats_0.54.0 Biobase_2.44.0
[16] GenomicRanges_1.36.0 GenomeInfoDb_1.20.0 IRanges_2.18.1 S4Vectors_0.22.0 BiocGenerics_0.30.0
loaded via a namespace (and not attached):
[1] backports_1.1.4 circlize_0.4.6 Hmisc_4.2-0 corrplot_0.84 aroma.light_3.14.0
[6] plyr_1.8.4 selectr_0.4-1 ConsensusClusterPlus_1.48.0 lazyeval_0.2.2 splines_3.6.0
[11] ggplot2_3.2.0 digest_0.6.20 foreach_1.4.4 ensembldb_2.8.0 htmltools_0.3.6
[16] magrittr_1.5 checkmate_1.9.4 memoise_1.1.0 BSgenome_1.52.0 cluster_2.0.8
[21] doParallel_1.0.14 ComplexHeatmap_2.0.0 Biostrings_2.52.0 readr_1.3.1 annotate_1.62.0
[26] R.utils_2.9.0 prettyunits_1.0.2 colorspace_1.4-1 blob_1.1.1 rvest_0.3.4
[31] ggrepel_0.8.1 xfun_0.8 dplyr_0.8.3 crayon_1.3.4 RCurl_1.95-4.12
[36] jsonlite_1.6 zoo_1.8-6 survival_2.44-1.1 VariantAnnotation_1.30.1 iterators_1.0.10
[41] glue_1.3.1 survminer_0.4.4 gtable_0.3.0 zlibbioc_1.30.0 XVector_0.24.0
[46] GetoptLong_0.1.7 shape_1.4.4 scales_1.0.0 DESeq_1.36.0 DBI_1.0.0
[51] ggthemes_4.2.0 Rcpp_1.0.1 viridisLite_0.3.0 cmprsk_2.2-8 xtable_1.8-4
[56] progress_1.2.2 htmlTable_1.13.1 clue_0.3-57 foreign_0.8-71 bit_1.1-14
[61] matlab_1.0.2 km.ci_0.5-2 Formula_1.2-3 htmlwidgets_1.3 httr_1.4.0
[66] RColorBrewer_1.1-2 acepack_1.4.1 reshape_0.8.8 pkgconfig_2.0.2 XML_3.98-1.20
[71] R.methodsS3_1.7.1 Gviz_1.28.0 nnet_7.3-12 locfit_1.5-9.1 tidyselect_0.2.5
[76] rlang_0.4.0 AnnotationDbi_1.46.0 munsell_0.5.0 tools_3.6.0 downloader_0.4
[81] generics_0.0.2 RSQLite_2.1.1 broom_0.5.2 evaluate_0.14 stringr_1.4.0
[86] yaml_2.2.0 knitr_1.23 bit64_0.9-7 survMisc_0.5.5 purrr_0.3.2
[91] AnnotationFilter_1.8.0 TCGAbiolinks_2.12.2 EDASeq_2.18.0 R.oo_1.22.0 xml2_1.2.0
[96] compiler_3.6.0 rstudioapi_0.10 plotly_4.9.0 curl_3.3 png_0.1-7
[101] ggsignif_0.5.0 tibble_2.1.3 geneplotter_1.62.0 stringi_1.4.3 GenomicFeatures_1.36.3
[106] lattice_0.20-38 ProtGenerics_1.16.0 Matrix_1.2-17 KMsurv_0.1-5 pillar_1.4.2
[111] GlobalOptions_0.1.0 data.table_1.12.2 bitops_1.0-6 rtracklayer_1.44.0 R6_2.4.0
[116] latticeExtra_0.6-28 hwriter_1.3.2 ShortRead_1.42.0 gridExtra_2.3 codetools_0.2-16
[121] dichromat_2.0-0 assertthat_0.2.1 rjson_0.2.20 GenomicAlignments_1.20.1 Rsamtools_2.0.0
[126] GenomeInfoDbData_1.2.1 hms_0.4.2 grid_3.6.0 rpart_4.1-15 tidyr_0.8.3
[131] rmarkdown_1.13 ggpubr_0.2.1 biovizBase_1.32.0 base64enc_0.1-3
Hi Tiago,
Thanks for your reply, unfortunately it appears to be the same (versions are now ELMER2.9.2, ELMER.data2.9.3 )
Thanks for the example, but it is working on my side that part of the code.
It is accessing ENSEMBL database using biomart. There was a change recently in one of the fields name. Please, could you try updating TCGAbiolinks and ELMER and try again. You should have ELMER 2.9.3 now.
That seems to have sorted it, thanks!