Working idea: This network will then be used to identify hub genes for each of the early, middle and late interactions.
library(WGCNA)
library(DESeq2)
library(GEOquery)
library(tidyverse)
library(gridExtra)
library(reshape2)
library(rtracklayer)
library(dplyr)
library(edgeR)
library("kableExtra")mtcars %>% kbl() %>% kable_paper()| mpg | cyl | disp | hp | drat | wt | qsec | vs | am | gear | carb | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| Mazda RX4 | 21.0 | 6 | 160.0 | 110 | 3.90 | 2.620 | 16.46 | 0 | 1 | 4 | 4 |
| Mazda RX4 Wag | 21.0 | 6 | 160.0 | 110 | 3.90 | 2.875 | 17.02 | 0 | 1 | 4 | 4 |
| Datsun 710 | 22.8 | 4 | 108.0 | 93 | 3.85 | 2.320 | 18.61 | 1 | 1 | 4 | 1 |
| Hornet 4 Drive | 21.4 | 6 | 258.0 | 110 | 3.08 | 3.215 | 19.44 | 1 | 0 | 3 | 1 |
| Hornet Sportabout | 18.7 | 8 | 360.0 | 175 | 3.15 | 3.440 | 17.02 | 0 | 0 | 3 | 2 |
| Valiant | 18.1 | 6 | 225.0 | 105 | 2.76 | 3.460 | 20.22 | 1 | 0 | 3 | 1 |
| Duster 360 | 14.3 | 8 | 360.0 | 245 | 3.21 | 3.570 | 15.84 | 0 | 0 | 3 | 4 |
| Merc 240D | 24.4 | 4 | 146.7 | 62 | 3.69 | 3.190 | 20.00 | 1 | 0 | 4 | 2 |
| Merc 230 | 22.8 | 4 | 140.8 | 95 | 3.92 | 3.150 | 22.90 | 1 | 0 | 4 | 2 |
| Merc 280 | 19.2 | 6 | 167.6 | 123 | 3.92 | 3.440 | 18.30 | 1 | 0 | 4 | 4 |
| Merc 280C | 17.8 | 6 | 167.6 | 123 | 3.92 | 3.440 | 18.90 | 1 | 0 | 4 | 4 |
| Merc 450SE | 16.4 | 8 | 275.8 | 180 | 3.07 | 4.070 | 17.40 | 0 | 0 | 3 | 3 |
| Merc 450SL | 17.3 | 8 | 275.8 | 180 | 3.07 | 3.730 | 17.60 | 0 | 0 | 3 | 3 |
| Merc 450SLC | 15.2 | 8 | 275.8 | 180 | 3.07 | 3.780 | 18.00 | 0 | 0 | 3 | 3 |
| Cadillac Fleetwood | 10.4 | 8 | 472.0 | 205 | 2.93 | 5.250 | 17.98 | 0 | 0 | 3 | 4 |
| Lincoln Continental | 10.4 | 8 | 460.0 | 215 | 3.00 | 5.424 | 17.82 | 0 | 0 | 3 | 4 |
| Chrysler Imperial | 14.7 | 8 | 440.0 | 230 | 3.23 | 5.345 | 17.42 | 0 | 0 | 3 | 4 |
| Fiat 128 | 32.4 | 4 | 78.7 | 66 | 4.08 | 2.200 | 19.47 | 1 | 1 | 4 | 1 |
| Honda Civic | 30.4 | 4 | 75.7 | 52 | 4.93 | 1.615 | 18.52 | 1 | 1 | 4 | 2 |
| Toyota Corolla | 33.9 | 4 | 71.1 | 65 | 4.22 | 1.835 | 19.90 | 1 | 1 | 4 | 1 |
| Toyota Corona | 21.5 | 4 | 120.1 | 97 | 3.70 | 2.465 | 20.01 | 1 | 0 | 3 | 1 |
| Dodge Challenger | 15.5 | 8 | 318.0 | 150 | 2.76 | 3.520 | 16.87 | 0 | 0 | 3 | 2 |
| AMC Javelin | 15.2 | 8 | 304.0 | 150 | 3.15 | 3.435 | 17.30 | 0 | 0 | 3 | 2 |
| Camaro Z28 | 13.3 | 8 | 350.0 | 245 | 3.73 | 3.840 | 15.41 | 0 | 0 | 3 | 4 |
| Pontiac Firebird | 19.2 | 8 | 400.0 | 175 | 3.08 | 3.845 | 17.05 | 0 | 0 | 3 | 2 |
| Fiat X1-9 | 27.3 | 4 | 79.0 | 66 | 4.08 | 1.935 | 18.90 | 1 | 1 | 4 | 1 |
| Porsche 914-2 | 26.0 | 4 | 120.3 | 91 | 4.43 | 2.140 | 16.70 | 0 | 1 | 5 | 2 |
| Lotus Europa | 30.4 | 4 | 95.1 | 113 | 3.77 | 1.513 | 16.90 | 1 | 1 | 5 | 2 |
| Ford Pantera L | 15.8 | 8 | 351.0 | 264 | 4.22 | 3.170 | 14.50 | 0 | 1 | 5 | 4 |
| Ferrari Dino | 19.7 | 6 | 145.0 | 175 | 3.62 | 2.770 | 15.50 | 0 | 1 | 5 | 6 |
| Maserati Bora | 15.0 | 8 | 301.0 | 335 | 3.54 | 3.570 | 14.60 | 0 | 1 | 5 | 8 |
| Volvo 142E | 21.4 | 4 | 121.0 | 109 | 4.11 | 2.780 | 18.60 | 1 | 1 | 4 | 2 |
## R version 4.3.0 (2023-04-21)
## Platform: x86_64-pc-linux-gnu (64-bit)
## Running under: Ubuntu 22.04.2 LTS
##
## Matrix products: default
## BLAS: /usr/lib/x86_64-linux-gnu/blas/libblas.so.3.10.0
## LAPACK: /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.10.0
##
## locale:
## [1] LC_CTYPE=en_AU.UTF-8 LC_NUMERIC=C
## [3] LC_TIME=en_AU.UTF-8 LC_COLLATE=en_AU.UTF-8
## [5] LC_MONETARY=en_AU.UTF-8 LC_MESSAGES=en_AU.UTF-8
## [7] LC_PAPER=en_AU.UTF-8 LC_NAME=C
## [9] LC_ADDRESS=C LC_TELEPHONE=C
## [11] LC_MEASUREMENT=en_AU.UTF-8 LC_IDENTIFICATION=C
##
## time zone: Australia/Melbourne
## tzcode source: system (glibc)
##
## attached base packages:
## [1] stats4 stats graphics grDevices utils datasets methods
## [8] base
##
## other attached packages:
## [1] kableExtra_1.3.4 edgeR_3.42.2
## [3] limma_3.56.0 rtracklayer_1.60.0
## [5] reshape2_1.4.4 gridExtra_2.3
## [7] lubridate_1.9.2 forcats_1.0.0
## [9] stringr_1.5.0 dplyr_1.1.2
## [11] purrr_1.0.1 readr_2.1.4
## [13] tidyr_1.3.0 tibble_3.2.1
## [15] ggplot2_3.4.2 tidyverse_2.0.0
## [17] GEOquery_2.68.0 DESeq2_1.40.1
## [19] SummarizedExperiment_1.30.1 Biobase_2.60.0
## [21] MatrixGenerics_1.12.0 matrixStats_0.63.0
## [23] GenomicRanges_1.52.0 GenomeInfoDb_1.36.0
## [25] IRanges_2.34.0 S4Vectors_0.38.1
## [27] BiocGenerics_0.46.0 WGCNA_1.72-1
## [29] fastcluster_1.2.3 dynamicTreeCut_1.63-1
##
## loaded via a namespace (and not attached):
## [1] rstudioapi_0.14 jsonlite_1.8.4 magrittr_2.0.3
## [4] rmarkdown_2.21 BiocIO_1.10.0 zlibbioc_1.46.0
## [7] vctrs_0.6.2 memoise_2.0.1 Rsamtools_2.16.0
## [10] RCurl_1.98-1.12 prettydoc_0.4.1 base64enc_0.1-3
## [13] webshot_0.5.4 htmltools_0.5.5 S4Arrays_1.0.1
## [16] Formula_1.2-5 sass_0.4.5 bslib_0.4.2
## [19] htmlwidgets_1.6.2 plyr_1.8.8 impute_1.74.1
## [22] cachem_1.0.7 GenomicAlignments_1.36.0 lifecycle_1.0.3
## [25] iterators_1.0.14 pkgconfig_2.0.3 Matrix_1.5-4
## [28] R6_2.5.1 fastmap_1.1.1 GenomeInfoDbData_1.2.10
## [31] digest_0.6.31 colorspace_2.1-0 AnnotationDbi_1.62.1
## [34] Hmisc_5.0-1 RSQLite_2.3.1 fansi_1.0.4
## [37] timechange_0.2.0 httr_1.4.5 compiler_4.3.0
## [40] bit64_4.0.5 withr_2.5.0 doParallel_1.0.17
## [43] htmlTable_2.4.1 backports_1.4.1 BiocParallel_1.34.0
## [46] DBI_1.1.3 highr_0.10 DelayedArray_0.26.1
## [49] rjson_0.2.21 tools_4.3.0 foreign_0.8-84
## [52] nnet_7.3-18 glue_1.6.2 restfulr_0.0.15
## [55] grid_4.3.0 checkmate_2.2.0 cluster_2.1.4
## [58] generics_0.1.3 gtable_0.3.3 tzdb_0.3.0
## [61] rmdformats_1.0.4 preprocessCore_1.62.1 data.table_1.14.8
## [64] hms_1.1.3 xml2_1.3.4 utf8_1.2.3
## [67] XVector_0.40.0 foreach_1.5.2 pillar_1.9.0
## [70] splines_4.3.0 lattice_0.21-8 survival_3.5-5
## [73] bit_4.0.5 tidyselect_1.2.0 GO.db_3.17.0
## [76] locfit_1.5-9.7 Biostrings_2.68.0 knitr_1.42
## [79] bookdown_0.33 svglite_2.1.1 xfun_0.39
## [82] stringi_1.7.12 yaml_2.3.7 evaluate_0.20
## [85] codetools_0.2-19 cli_3.6.1 rpart_4.1.19
## [88] systemfonts_1.0.4 munsell_0.5.0 jquerylib_0.1.4
## [91] Rcpp_1.0.10 png_0.1-8 XML_3.99-0.14
## [94] parallel_4.3.0 blob_1.2.4 bitops_1.0-7
## [97] viridisLite_0.4.1 scales_1.2.1 crayon_1.5.2
## [100] rlang_1.1.1 KEGGREST_1.40.0 rvest_1.0.3