Question: problem on getpromoters on hg38
0
gravatar for jarod_v6@libero.it
18 months ago by
Italy
jarod_v6@libero.it40 wrote:

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

 

 

chipseeker • 393 views
ADD COMMENTlink written 18 months ago by jarod_v6@libero.it40
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