Last updated: 2026-01-15
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Knit directory: DXR_continue/
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library(tidyverse)
library(GenomicRanges)
library(plyranges)
library(genomation)
library(readr)
library(rtracklayer)
library(stringr)
library(ggrepel)
library(DT)
library(readxl)adding in data files.
The current analysis should be RNA DEGs and ROIs by set expression levels. more steps will include viewing the association of DEGs with enrichment/depeletion of ROIs containing TEs by class/familiy with a look at age.
###Loading all ROIs, already out by Set and combined
H3K27ac_anno_ROIs <- readRDS("data/motif_lists/H3K27ac_annotated_peaks.RDS")
## Loading single summit locations and adding in
H3K27ac_summit_gr <- readRDS("data/RDS_files/H3K27ac_complete_summit_gr.RDS")
##assigning Peakid as name of summit region
mcols(H3K27ac_summit_gr)$name <- mcols(H3K27ac_summit_gr)$Peakid
## Creating a lookup file if needed
H3K27ac_lookup <- imap_dfr(H3K27ac_anno_ROIs[1:3], ~
tibble(Peakid = .x@anno$Peakid, cluster = .y)
)
RNA_full_toptable <- readRDS("data/Other_paper_data/RNA_full_toptable.RDS")
RNA_cluster_lookup<- readRDS( "data/Other_paper_data/RNA_cluster_lookup.RDS")##For my reference only
### Loading in RNA expression data
RNA_toptable_24T <- read_excel("C:/Users/renee/Other_projects_data/DXR_data/DXR_RNA_data/Pfortmiller_S2_Appendix_251213.xlsx",
sheet = "Table_S3", skip = 1)
RNA_toptable_24R <- read_excel("C:/Users/renee/Other_projects_data/DXR_data/DXR_RNA_data/Pfortmiller_S2_Appendix_251213.xlsx",
sheet = "Table_S4", skip = 1)
RNA_toptable_144R <- read_excel("C:/Users/renee/Other_projects_data/DXR_data/DXR_RNA_data/Pfortmiller_S2_Appendix_251213.xlsx",
sheet = "Table_S5", skip = 1)
RNA_acute_cluster <- read_excel("C:/Users/renee/Other_projects_data/DXR_data/DXR_RNA_data/Pfortmiller_S2_Appendix_251213.xlsx",
sheet = "Table_S6", skip = 1)
RNA_chronic_cluster <- read_excel("C:/Users/renee/Other_projects_data/DXR_data/DXR_RNA_data/Pfortmiller_S2_Appendix_251213.xlsx",
sheet = "Table_S7", skip = 2)
## Creating R object for my data:
RNA_full_toptable <- RNA_toptable_24T %>%
mutate(timepoint="24T") %>%
bind_rows(., (RNA_toptable_24R %>%
mutate(timepoint="24R"))) %>%
bind_rows(., (RNA_toptable_144R %>%
mutate(timepoint="144R")))
# saveRDS(RNA_full_toptable, "data/Other_paper_data/RNA_full_toptable.RDS")
RNA_cluster_lookup <- RNA_acute_cluster %>%
mutate(Response_Direction="NA") %>%
bind_rows(RNA_chronic_cluster)
# saveRDS(RNA_cluster_lookup, "data/Other_paper_data/RNA_cluster_lookup.RDS")
sessionInfo()R version 4.4.2 (2024-10-31 ucrt)
Platform: x86_64-w64-mingw32/x64
Running under: Windows 11 x64 (build 26200)
Matrix products: default
locale:
[1] LC_COLLATE=English_United States.utf8
[2] LC_CTYPE=English_United States.utf8
[3] LC_MONETARY=English_United States.utf8
[4] LC_NUMERIC=C
[5] LC_TIME=English_United States.utf8
time zone: America/Chicago
tzcode source: internal
attached base packages:
[1] grid stats4 stats graphics grDevices utils datasets
[8] methods base
other attached packages:
[1] readxl_1.4.5 DT_0.33 ggrepel_0.9.6
[4] rtracklayer_1.66.0 genomation_1.38.0 plyranges_1.26.0
[7] GenomicRanges_1.58.0 GenomeInfoDb_1.42.3 IRanges_2.40.1
[10] S4Vectors_0.44.0 BiocGenerics_0.52.0 lubridate_1.9.4
[13] forcats_1.0.0 stringr_1.5.1 dplyr_1.1.4
[16] purrr_1.1.0 readr_2.1.5 tidyr_1.3.1
[19] tibble_3.3.0 ggplot2_3.5.2 tidyverse_2.0.0
[22] workflowr_1.7.1
loaded via a namespace (and not attached):
[1] bitops_1.0-9 rlang_1.1.6
[3] magrittr_2.0.3 git2r_0.36.2
[5] gridBase_0.4-7 matrixStats_1.5.0
[7] compiler_4.4.2 getPass_0.2-4
[9] callr_3.7.6 vctrs_0.6.5
[11] reshape2_1.4.4 pkgconfig_2.0.3
[13] crayon_1.5.3 fastmap_1.2.0
[15] XVector_0.46.0 Rsamtools_2.22.0
[17] promises_1.3.3 rmarkdown_2.29
[19] tzdb_0.5.0 UCSC.utils_1.2.0
[21] ps_1.9.1 xfun_0.52
[23] zlibbioc_1.52.0 cachem_1.1.0
[25] jsonlite_2.0.0 later_1.4.2
[27] DelayedArray_0.32.0 BiocParallel_1.40.2
[29] parallel_4.4.2 R6_2.6.1
[31] bslib_0.9.0 stringi_1.8.7
[33] RColorBrewer_1.1-3 cellranger_1.1.0
[35] jquerylib_0.1.4 Rcpp_1.1.0
[37] SummarizedExperiment_1.36.0 knitr_1.50
[39] httpuv_1.6.16 Matrix_1.7-3
[41] timechange_0.3.0 tidyselect_1.2.1
[43] rstudioapi_0.17.1 dichromat_2.0-0.1
[45] abind_1.4-8 yaml_2.3.10
[47] seqPattern_1.38.0 codetools_0.2-20
[49] curl_7.0.0 processx_3.8.6
[51] lattice_0.22-7 plyr_1.8.9
[53] Biobase_2.66.0 withr_3.0.2
[55] evaluate_1.0.5 Biostrings_2.74.1
[57] pillar_1.11.0 MatrixGenerics_1.18.1
[59] whisker_0.4.1 KernSmooth_2.23-26
[61] generics_0.1.4 rprojroot_2.1.1
[63] RCurl_1.98-1.17 hms_1.1.3
[65] scales_1.4.0 glue_1.8.0
[67] tools_4.4.2 BiocIO_1.16.0
[69] data.table_1.17.8 BSgenome_1.74.0
[71] GenomicAlignments_1.42.0 fs_1.6.6
[73] XML_3.99-0.18 impute_1.80.0
[75] plotrix_3.8-4 colorspace_2.1-1
[77] GenomeInfoDbData_1.2.13 restfulr_0.0.16
[79] cli_3.6.5 S4Arrays_1.6.0
[81] gtable_0.3.6 sass_0.4.10
[83] digest_0.6.37 SparseArray_1.6.2
[85] htmlwidgets_1.6.4 rjson_0.2.23
[87] farver_2.1.2 htmltools_0.5.8.1
[89] lifecycle_1.0.4 httr_1.4.7