esATAC Report for Case and Control
Zheng Wei and Wei Zhang
2018-02-15
load("Report2.Rdata")1 Case Control Peak Compare
The following is the peak comparation result for case and control.
The total peaks in case are 4709, specific peaks in case are 3831.
The total peaks in control are 4660, specific peaks in control are 3787.
The overlap peaks are merged to 849 peaks.
2 GO Analysis
Gene ontology analysis for all genes around specific peak regions of case and control.
2.1 Significant GO terms of genes associated with case specific peaks
## [1] "No GO terms found: empty table"2.2 Significant GO terms of genes associated with control specific peaks
## [1] "No GO terms found: empty table"3 Motif Enrichment Analysis
This function takes case and control specific peaks as foreground respectively, overlap peaks between case and control as background.
3.1 Significant motifs of case specific peaks
| motif | motif length | p_value |
|---|---|---|
| CTCF | 19 | 0.148 |
3.2 Significant motifs of control specific peaks
| motif | motif length | p_value |
|---|---|---|
| CTCF | 19 | 0.0277 |
4 Genomic Footprint
The following is the footprint for motif occurance of case&control peaks.
For all footprint of case sample, The absolute path is /home/zwei/esATAC_test/pkgRepCC/esATAC_pipeline/intermediate_results/case/rep_concord_merge/Footprint_Case_data/FP_PDF_Case_data.
For all footprint of control sample, The absolute path is /home/zwei/esATAC_test/pkgRepCC/esATAC_pipeline/intermediate_results/control/rep_concord_merge/Footprint_Control_data/FP_PDF_Control_data.
The following is the footprint for motif occurance of case&control specific peaks.
For all footprint of case specific, The absolute path is /home/zwei/esATAC_test/pkgRepCC/esATAC_pipeline/intermediate_results/case_control/Footprint_Case_specific/FP_PDF_Case_specific.
For all footprint of control specific, The absolute path is /home/zwei/esATAC_test/pkgRepCC/esATAC_pipeline/intermediate_results/case_control/Footprint_Control_specific/FP_PDF_Control_specific.
5 Session Info
sessionInfo()## R version 3.4.3 (2017-11-30)
## Platform: x86_64-pc-linux-gnu (64-bit)
## Running under: Red Hat Enterprise Linux Server 7.2 (Maipo)
##
## Matrix products: default
## BLAS: /home/software/R/R-3.4.3/lib64/R/lib/libRblas.so
## LAPACK: /home/software/R/R-3.4.3/lib64/R/lib/libRlapack.so
##
## locale:
## [1] LC_CTYPE=en_US.utf8 LC_NUMERIC=C
## [3] LC_TIME=en_US.utf8 LC_COLLATE=en_US.utf8
## [5] LC_MONETARY=en_US.utf8 LC_MESSAGES=en_US.utf8
## [7] LC_PAPER=en_US.utf8 LC_NAME=en_US.utf8
## [9] LC_ADDRESS=en_US.utf8 LC_TELEPHONE=en_US.utf8
## [11] LC_MEASUREMENT=en_US.utf8 LC_IDENTIFICATION=en_US.utf8
##
## attached base packages:
## [1] grid stats4 parallel methods stats graphics grDevices
## [8] utils datasets base
##
## other attached packages:
## [1] corrplot_0.84
## [2] VennDiagram_1.6.18
## [3] futile.logger_1.4.3
## [4] ChIPseeker_1.14.1
## [5] gridExtra_2.3
## [6] ggplot2_2.2.1
## [7] TxDb.Hsapiens.UCSC.hg19.knownGene_3.2.2
## [8] GenomicFeatures_1.30.3
## [9] org.Hs.eg.db_3.5.0
## [10] AnnotationDbi_1.40.0
## [11] BSgenome.Hsapiens.UCSC.hg19_1.4.0
## [12] BSgenome_1.46.0
## [13] rtracklayer_1.38.3
## [14] esATAC_1.0.17
## [15] ShortRead_1.36.0
## [16] GenomicAlignments_1.14.1
## [17] SummarizedExperiment_1.8.1
## [18] DelayedArray_0.4.1
## [19] matrixStats_0.53.1
## [20] Biobase_2.38.0
## [21] BiocParallel_1.12.0
## [22] Rsamtools_1.30.0
## [23] Biostrings_2.46.0
## [24] XVector_0.18.0
## [25] GenomicRanges_1.30.1
## [26] GenomeInfoDb_1.14.0
## [27] IRanges_2.12.0
## [28] S4Vectors_0.16.0
## [29] BiocGenerics_0.24.0
##
## loaded via a namespace (and not attached):
## [1] backports_1.1.2 fastmatch_1.1-0
## [3] VGAM_1.0-5 plyr_1.8.4
## [5] igraph_1.1.2 lazyeval_0.2.1
## [7] splines_3.4.3 gridBase_0.4-7
## [9] TFBSTools_1.16.0 digest_0.6.15
## [11] BiocInstaller_1.28.0 htmltools_0.3.6
## [13] GOSemSim_2.4.1 viridis_0.5.0
## [15] GO.db_3.5.0 gdata_2.18.0
## [17] magrittr_1.5 memoise_1.1.0
## [19] JASPAR2016_1.6.0 readr_1.1.1
## [21] annotate_1.56.1 R.utils_2.6.0
## [23] prettyunits_1.0.2 colorspace_1.3-2
## [25] blob_1.1.0 dplyr_0.7.4
## [27] RCurl_1.95-4.10 jsonlite_1.5
## [29] bindr_0.1 TFMPvalue_0.0.6
## [31] brew_1.0-6 glue_1.2.0
## [33] gtable_0.2.0 zlibbioc_1.24.0
## [35] UpSetR_1.3.3 Rook_1.1-1
## [37] scales_0.5.0 DOSE_3.4.0
## [39] futile.options_1.0.0 DBI_0.7
## [41] Rcpp_0.12.15 plotrix_3.7
## [43] viridisLite_0.3.0 xtable_1.8-2
## [45] progress_1.1.2 bit_1.1-12
## [47] htmlwidgets_1.0 httr_1.3.1
## [49] DiagrammeR_0.9.2 fgsea_1.4.1
## [51] gplots_3.0.1 RColorBrewer_1.1-2
## [53] pkgconfig_2.0.1 XML_3.98-1.9
## [55] rJava_0.9-9 R.methodsS3_1.7.1
## [57] labeling_0.3 rlang_0.1.6
## [59] reshape2_1.4.3 munsell_0.4.3
## [61] tools_3.4.3 visNetwork_2.0.3
## [63] downloader_0.4 DirichletMultinomial_1.20.0
## [65] RSQLite_2.0 evaluate_0.10.1
## [67] stringr_1.2.0 yaml_2.1.16
## [69] knitr_1.19 bit64_0.9-7
## [71] caTools_1.17.1 purrr_0.2.4
## [73] KEGGREST_1.18.1 bindrcpp_0.2
## [75] R.oo_1.21.0 poweRlaw_0.70.1
## [77] DO.db_2.9 biomaRt_2.34.2
## [79] compiler_3.4.3 rstudioapi_0.7
## [81] rgexf_0.15.3 png_0.1-7
## [83] Rbowtie2_1.0.1 tibble_1.4.2
## [85] stringi_1.1.6 highr_0.6
## [87] lattice_0.20-35 CNEr_1.14.0
## [89] Matrix_1.2-12 pillar_1.1.0
## [91] data.table_1.10.4-3 bitops_1.0-6
## [93] qvalue_2.10.0 R6_2.2.2
## [95] latticeExtra_0.6-28 hwriter_1.3.2
## [97] RMySQL_0.10.13 KernSmooth_2.23-15
## [99] lambda.r_1.2 boot_1.3-20
## [101] gtools_3.5.0 assertthat_0.2.0
## [103] seqLogo_1.44.0 rprojroot_1.3-2
## [105] GenomeInfoDbData_1.0.0 hms_0.4.1
## [107] influenceR_0.1.0 clusterProfiler_3.6.0
## [109] tidyr_0.8.0 rmarkdown_1.8
## [111] rvcheck_0.0.9