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I use this code and seem I ca'nt filter only protein coding genes. If I use values= ret$ensembl the operation works well. How can resolve this problem ensembl = useMart( host="dec2017.archive.ensembl.org", biomart="ENSEMBL_MART_ENSEMBL", dataset = "hsapiens_gene_ensembl" ) genemap <- getBM( attributes = c("ensembl_gene_id", "hgnc_symbol","family","gene_biotype","family_description"), filters = "ensembl_gene_id", values = list(ret$ensembl,"protein_coding"), mart = ensembl )
> sessionInfo() R version 3.4.4 (2018-03-15) Platform: x86_64-pc-linux-gnu (64-bit) Running under: Ubuntu 16.04.4 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_US.UTF-8 LC_NUMERIC=C LC_TIME=it_IT.UTF-8 LC_COLLATE=en_US.UTF-8 [5] LC_MONETARY=it_IT.UTF-8 LC_MESSAGES=en_US.UTF-8 LC_PAPER=it_IT.UTF-8 LC_NAME=C [9] LC_ADDRESS=C LC_TELEPHONE=C LC_MEASUREMENT=it_IT.UTF-8 LC_IDENTIFICATION=C attached base packages: [1] grid parallel stats4 stats graphics grDevices utils datasets methods base other attached packages: [1] ComplexHeatmap_1.17.1 gplots_3.0.1 biomaRt_2.34.2 limma_3.34.9 [5] pheatmap_1.0.8 genefilter_1.60.0 reshape2_1.4.3 RColorBrewer_1.1-2 [9] ggplot2_2.2.1 DESeq2_1.18.1 SummarizedExperiment_1.8.1 DelayedArray_0.4.1 [13] matrixStats_0.53.1 Biobase_2.38.0 GenomicRanges_1.30.3 GenomeInfoDb_1.14.0 [17] IRanges_2.12.0 S4Vectors_0.16.0 BiocGenerics_0.24.0 loaded via a namespace (and not attached): [1] httr_1.3.1 bit64_0.9-7 splines_3.4.4 gtools_3.5.0 Formula_1.2-3 [6] assertthat_0.2.0 latticeExtra_0.6-28 blob_1.1.1 GenomeInfoDbData_1.0.0 progress_1.1.2 [11] pillar_1.2.2 RSQLite_2.1.1 backports_1.1.2 lattice_0.20-35 digest_0.6.15 [16] XVector_0.18.0 checkmate_1.8.5 colorspace_1.3-2 htmltools_0.3.6 Matrix_1.2-14 [21] plyr_1.8.4 XML_3.98-1.11 GetoptLong_0.1.6 zlibbioc_1.24.0 xtable_1.8-2 [26] scales_0.5.0 gdata_2.18.0 BiocParallel_1.12.0 htmlTable_1.11.2 tibble_1.4.2 [31] annotate_1.56.2 nnet_7.3-12 lazyeval_0.2.1 survival_2.42-3 magrittr_1.5 [36] memoise_1.1.0 foreign_0.8-70 tools_3.4.4 data.table_1.11.2 prettyunits_1.0.2 [41] GlobalOptions_0.0.13 stringr_1.3.1 munsell_0.4.3 locfit_1.5-9.1 cluster_2.0.7-1 [46] AnnotationDbi_1.40.0 compiler_3.4.4 caTools_1.17.1 rlang_0.2.0 RCurl_1.95-4.10 [51] rstudioapi_0.7 circlize_0.4.3 rjson_0.2.18 htmlwidgets_1.2 bitops_1.0-6 [56] base64enc_0.1-3 gtable_0.2.0 curl_3.2 DBI_1.0.0 R6_2.2.2 [61] gridExtra_2.3 knitr_1.20 bit_1.1-12 Hmisc_4.1-1 shape_1.4.4 [66] KernSmooth_2.23-15 stringi_1.2.2 Rcpp_0.12.16 geneplotter_1.56.0 rpart_4.1-13 [71] acepack_1.4.1