Sample1.bed

Bed file: example-data/Sample1.bed

TSS distance: 3000

Sample2.bed

Bed file: example-data/Sample2.bed

TSS distance: 3000

peaks.bed

Bed file: example-data/Sample4/peaks.bed

TSS distance: 3000

Session Info

## System location:  
## /ifs/home/kellys04/projects/test/peak-type-summaryGit Remote:  
## origin   git@github.com:stevekm/peak-type-summary.git (fetch)  
##  Git Remote:  
## origin   git@github.com:stevekm/peak-type-summary.git (push)  
## Git branch and commit  
## report: 4dd388f5260b8b5a2a4106de871ab35414f12c45Time and Date of report creation:  
## Mon Oct  9 19:57:58 EDT 2017R version 3.3.0 (2016-05-03)
## Platform: x86_64-pc-linux-gnu (64-bit)
## Running under: CentOS release 6.8 (Final)
## 
## locale:
## [1] C
## 
## attached base packages:
##  [1] stats4    parallel  methods   grid      tools     stats     graphics 
##  [8] grDevices utils     datasets  base     
## 
## other attached packages:
##  [1] org.Hs.eg.db_3.3.0                     
##  [2] TxDb.Hsapiens.UCSC.hg19.knownGene_3.2.2
##  [3] GenomicFeatures_1.24.5                 
##  [4] AnnotationDbi_1.34.4                   
##  [5] Biobase_2.32.0                         
##  [6] GenomicRanges_1.24.3                   
##  [7] GenomeInfoDb_1.8.7                     
##  [8] IRanges_2.6.1                          
##  [9] S4Vectors_0.10.3                       
## [10] BiocGenerics_0.18.0                    
## [11] clusterProfiler_3.0.5                  
## [12] DOSE_2.10.7                            
## [13] ChIPseeker_1.8.9                       
## [14] gridExtra_2.2.1                        
## [15] optparse_1.4.4                         
## 
## loaded via a namespace (and not attached):
##  [1] bitops_1.0-6               matrixStats_0.52.2        
##  [3] bit64_0.9-7                RColorBrewer_1.1-2        
##  [5] rprojroot_1.2              UpSetR_1.3.3              
##  [7] backports_1.1.0            R6_2.2.2                  
##  [9] KernSmooth_2.23-15         DBI_0.7                   
## [11] lazyeval_0.2.0             colorspace_1.3-2          
## [13] bit_1.1-12                 graph_1.50.0              
## [15] SparseM_1.77               labeling_0.3              
## [17] rtracklayer_1.32.2         topGO_2.24.0              
## [19] caTools_1.17.1             scales_0.4.1              
## [21] stringr_1.2.0              digest_0.6.12             
## [23] Rsamtools_1.24.0           rmarkdown_1.6             
## [25] XVector_0.12.1             pkgconfig_2.0.1           
## [27] htmltools_0.3.6            plotrix_3.6-5             
## [29] rlang_0.1.1                RSQLite_2.0               
## [31] bindr_0.1                  BiocParallel_1.6.6        
## [33] gtools_3.5.0               GOSemSim_1.30.3           
## [35] dplyr_0.7.2                RCurl_1.95-4.8            
## [37] magrittr_1.5               GO.db_3.3.0               
## [39] Rcpp_0.12.12               munsell_0.4.3             
## [41] stringi_1.1.5              yaml_2.1.14               
## [43] SummarizedExperiment_1.2.3 zlibbioc_1.18.0           
## [45] gplots_3.0.1               plyr_1.8.4                
## [47] qvalue_2.4.2               blob_1.1.0                
## [49] gdata_2.18.0               DO.db_2.9                 
## [51] lattice_0.20-35            Biostrings_2.40.2         
## [53] splines_3.3.0              annotate_1.50.1           
## [55] knitr_1.16                 igraph_1.1.2              
## [57] boot_1.3-19                reshape2_1.4.2            
## [59] biomaRt_2.28.0             XML_3.98-1.9              
## [61] glue_1.1.1                 evaluate_0.10.1           
## [63] gtable_0.2.0               getopt_1.20.0             
## [65] tidyr_0.6.3                assertthat_0.2.0          
## [67] ggplot2_2.2.1              gridBase_0.4-7            
## [69] xtable_1.8-2               tibble_1.3.3              
## [71] GenomicAlignments_1.8.4    memoise_1.1.0             
## [73] bindrcpp_0.2               GSEABase_1.34.1           
##                               sysname 
##                               "Linux" 
##                               release 
##          "2.6.32-642.11.1.el6.x86_64" 
##                               version 
## "#1 SMP Fri Nov 18 19:25:05 UTC 2016" 
##                              nodename 
##                            "phoenix2" 
##                               machine 
##                              "x86_64" 
##                                 login 
##                            "kellys04" 
##                                  user 
##                            "kellys04" 
##                        effective_user 
##                            "kellys04"