Last updated: 2021-02-19
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Knit directory: Human_Development_ATACseq_bulk/
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| Rmd | 294d830 | evangelynsim | 2021-02-19 | wflow_publish(c(“analysis/01.Generate_reference_genome.Rmd”, |
To investigate the correlation between ATAC-seq and RNA-seq, ATAC-seq sequencing reads were mapped to 1kbp up-/down-stream of transcription start site to identify associated genes.
The result were then subjected to EdgeR differential expression analysis and then correlated with RNA-seq EdgeR outcomes.
library(edgeR)Loading required package: limmalibrary(limma)
library(dplyr)
Attaching package: 'dplyr'The following objects are masked from 'package:stats':
filter, lagThe following objects are masked from 'package:base':
intersect, setdiff, setequal, unionlibrary(ggplot2)
library(moonBook)
library(webr)
library(waffle)
library(extrafont)Registering fonts with Rlibrary(grid)
library(gridExtra)
Attaching package: 'gridExtra'The following object is masked from 'package:dplyr':
combinelibrary(cowplot)
********************************************************Note: As of version 1.0.0, cowplot does not change the default ggplot2 theme anymore. To recover the previous behavior, execute:
theme_set(theme_cowplot())********************************************************library(ggpubr)
Attaching package: 'ggpubr'The following object is masked from 'package:cowplot':
get_legendlibrary(RColorBrewer)#!/bin/bash
join -1 1 -2 1 <(sort -k 1b,1 edgeR_ATAC_1kbTSS_all_hum_Development_noXY.xls.rnk) <(sort -k 1b,1 edgeR_RNA_mina12a13y5y6_Development_noXY.xls.rnk) | tr ' ' '\t' > Development_noXY.jn.rnk
join -1 1 -2 1 <(sort -k 1b,1 edgeR_ATAC_1kbTSS_all_hum_FetalvsYoung_noXY.xls.rnk) <(sort -k 1b,1 edgeR_RNA_mina12a13y5y6_FetalvsYoung_noXY.xls.rnk) | tr ' ' '\t' > FetalvsYoung_noXY.jn.rnk
join -1 1 -2 1 <(sort -k 1b,1 edgeR_ATAC_1kbTSS_all_hum_YoungvsAdult_noXY.xls.rnk) <(sort -k 1b,1 edgeR_RNA_mina12a13y5y6_YoungvsAdult_noXY.xls.rnk) | tr ' ' '\t' > YoungvsAdult_noXY.jn.rnkSource code for integration and enrichment analysis
source("EnDrich.R", local = knitr::knit_global())Developmental data
source("EnDrichProc_Development_noXY.R", local = knitr::knit_global())Fetal vs. Young data
source("EnDrichProc_FetalvsYoung_noXY.R", local = knitr::knit_global())Young vs. Adult data
source("EnDrichProc_YoungvsAdult_noXY.R", local = knitr::knit_global())
sessionInfo()R version 3.6.1 (2019-07-05)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: CentOS Linux 7 (Core)
Matrix products: default
BLAS: /hpc/software/installed/R/3.6.1/lib64/R/lib/libRblas.so
LAPACK: /hpc/software/installed/R/3.6.1/lib64/R/lib/libRlapack.so
locale:
[1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C
[3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8
[5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8
[7] LC_PAPER=en_US.UTF-8 LC_NAME=C
[9] LC_ADDRESS=C LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
attached base packages:
[1] grid stats graphics grDevices utils datasets methods
[8] base
other attached packages:
[1] RColorBrewer_1.1-2 ggpubr_0.4.0 cowplot_1.0.0 gridExtra_2.3
[5] extrafont_0.17 waffle_0.7.0 webr_0.1.5 moonBook_0.2.3
[9] ggplot2_3.3.2 dplyr_1.0.2 edgeR_3.26.8 limma_3.40.6
[13] workflowr_1.6.2
loaded via a namespace (and not attached):
[1] nlme_3.1-150 fs_1.5.0 insight_0.9.0 rprojroot_1.3-2
[5] tools_3.6.1 backports_1.1.10 R6_2.5.0 DT_0.14
[9] sjlabelled_1.1.6 colorspace_1.4-1 withr_2.3.0 tidyselect_1.1.0
[13] mnormt_1.5-6 extrafontdb_1.0 curl_4.3 compiler_3.6.1
[17] git2r_0.27.1 flextable_0.5.10 xml2_1.3.2 officer_0.3.12
[21] scales_1.1.1 lmtest_0.9-38 psych_1.9.12.31 readr_1.4.0
[25] systemfonts_0.2.3 stringr_1.4.0 digest_0.6.27 foreign_0.8-71
[29] editData_0.1.2 rmarkdown_2.5 rio_0.5.16 base64enc_0.1-3
[33] pkgconfig_2.0.3 htmltools_0.5.0 fastmap_1.0.1 rvg_0.2.5
[37] htmlwidgets_1.5.2 rlang_0.4.7 readxl_1.3.1 rstudioapi_0.11
[41] shiny_1.5.0 farver_2.0.3 generics_0.1.0 zoo_1.8-8
[45] jsonlite_1.7.0 zip_2.1.1 car_3.0-10 magrittr_1.5
[49] Rcpp_1.0.5 munsell_0.5.0 abind_1.4-5 gdtools_0.2.2
[53] lifecycle_0.2.0 stringi_1.5.3 whisker_0.4 yaml_2.2.1
[57] carData_3.0-4 MASS_7.3-51.6 parallel_3.6.1 promises_1.1.1
[61] sjmisc_2.8.5 forcats_0.5.0 crayon_1.3.4 miniUI_0.1.1.1
[65] lattice_0.20-41 haven_2.3.1 hms_0.5.3 locfit_1.5-9.4
[69] knitr_1.30 pillar_1.4.6 uuid_0.1-4 ggsignif_0.6.0
[73] glue_1.4.2 evaluate_0.14 data.table_1.13.2 vcd_1.4-8
[77] vctrs_0.3.2 tweenr_1.0.1 httpuv_1.5.4 Rttf2pt1_1.3.8
[81] cellranger_1.1.0 gtable_0.3.0 purrr_0.3.4 polyclip_1.10-0
[85] tidyr_1.1.2 xfun_0.18 ggforce_0.3.2 openxlsx_4.2.3
[89] mime_0.9 xtable_1.8-4 broom_0.7.0 rstatix_0.6.0
[93] later_1.1.0.1 tibble_3.0.3 shinyWidgets_0.5.4 rrtable_0.2.1
[97] ellipsis_0.3.1 ztable_0.2.0 devEMF_3.8