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I try to use ChIPseeker I have peaks anntated with hg38.
library("ChIPseeker") library("TxDb.Hsapiens.UCSC.hg38.knownGene") setwd("~/Desktop/RESULTS2rip/") files=list.files("chr_hg38",full.names=T) files txdb <- TxDb.Hsapiens.UCSC.hg38.knownGene peakfile=readPeakFile(files[1]) promoter <- getPromoters(TxDb=txdb, upstream=3000, downstream=3000) Error in `seqlevels<-`(`*tmp*`, force = TRUE, value = c("chr1", "chr2", : unused argument (force = TRUE) > sessionInfo() R version 3.4.1 (2017-06-30) Platform: x86_64-pc-linux-gnu (64-bit) Running under: Ubuntu 16.04.3 LTS Matrix products: default BLAS: /home/maurizio/miniconda2/envs/delete/lib/R/lib/libRblas.so LAPACK: /home/maurizio/miniconda2/envs/delete/lib/R/lib/libRlapack.so locale: [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C LC_TIME=it_IT.UTF-8 [4] LC_COLLATE=en_US.UTF-8 LC_MONETARY=it_IT.UTF-8 LC_MESSAGES=en_US.UTF-8 [7] LC_PAPER=it_IT.UTF-8 LC_NAME=C LC_ADDRESS=C [10] LC_TELEPHONE=C LC_MEASUREMENT=it_IT.UTF-8 LC_IDENTIFICATION=C attached base packages: [1] stats4 parallel stats graphics grDevices utils datasets methods base other attached packages: [1] TxDb.Hsapiens.UCSC.hg38.knownGene_3.4.0 GenomicFeatures_1.26.4 [3] AnnotationDbi_1.40.0 Biobase_2.38.0 [5] GenomicRanges_1.30.0 GenomeInfoDb_1.14.0 [7] IRanges_2.12.0 S4Vectors_0.16.0 [9] BiocGenerics_0.24.0 ChIPseeker_1.14.0 loaded via a namespace (and not attached): [1] bit64_0.9-7 splines_3.4.1 [3] gtools_3.5.0 assertthat_0.2.0 [5] DO.db_2.9 rvcheck_0.0.9 [7] blob_1.1.0 GenomeInfoDbData_1.0.0 [9] Rsamtools_1.30.0 pillar_1.1.0 [11] RSQLite_2.0 lattice_0.20-35 [13] glue_1.2.0 digest_0.6.15 [15] RColorBrewer_1.1-2 XVector_0.18.0 [17] qvalue_2.10.0 colorspace_1.3-2 [19] Matrix_1.2-12 plyr_1.8.4 [21] XML_3.98-1.10 pkgconfig_2.0.1 [23] biomaRt_2.32.1 zlibbioc_1.24.0 [25] GO.db_3.5.0 scales_0.5.0 [27] gdata_2.18.0 BiocParallel_1.12.0 [29] tibble_1.4.2 ggplot2_2.2.1 [31] UpSetR_1.3.3 SummarizedExperiment_1.4.0 [33] lazyeval_0.2.1 magrittr_1.5 [35] memoise_1.1.0 DOSE_3.4.0 [37] gplots_3.0.1 tools_3.4.1 [39] data.table_1.10.4-3 gridBase_0.4-7 [41] stringr_1.3.0 munsell_0.4.3 [43] plotrix_3.6-6 bindrcpp_0.2 [45] Biostrings_2.46.0 compiler_3.4.1 [47] caTools_1.17.1 rlang_0.2.0 [49] grid_3.4.1 RCurl_1.95-4.10 [51] igraph_1.1.2 bitops_1.0-6 [53] boot_1.3-20 gtable_0.2.0 [55] DBI_0.7 reshape2_1.4.3 [57] R6_2.2.2 GenomicAlignments_1.10.0 [59] gridExtra_2.3 dplyr_0.7.4 [61] rtracklayer_1.38.0 bit_1.1-12 [63] bindr_0.1 fastmatch_1.1-0 [65] fgsea_1.4.0 KernSmooth_2.23-15 [67] GOSemSim_2.4.0 stringi_1.1.6 [69] TxDb.Hsapiens.UCSC.hg19.knownGene_3.2.2 Rcpp_0.12.15