library(tRavis)
#> Thanks for using tRavis v0.73.20! If you encounter any bugs
#> or problems, please submit an issue at the Github page:
#> https://github.com/travis-m-blimkie/tRavis/issues
tr_clean_deseq_results
ex_deseq_results <-
readRDS(system.file("extdata", "ex_deseq_results.rds", package = "tRavis"))
ex_deseq_results
#> log2 fold change (MLE): condition B vs A
#> Wald test p-value: condition B vs A
#> DataFrame with 200 rows and 6 columns
#> baseMean log2FoldChange lfcSE stat pvalue padj
#> <numeric> <numeric> <numeric> <numeric> <numeric> <numeric>
#> gene1 7.1530 -0.636105 0.750697 -0.847352 3.96799e-01 4.95998e-01
#> gene2 108.3659 2.872486 0.357737 8.029601 9.77899e-16 1.62983e-14
#> gene3 25.1923 1.724502 0.643106 2.681522 7.32882e-03 1.62863e-02
#> gene4 110.2302 -1.375727 0.321775 -4.275440 1.90761e-05 7.06521e-05
#> gene5 15.1829 -5.412610 0.819823 -6.602166 4.05195e-11 3.68359e-10
#> ... ... ... ... ... ... ...
#> gene196 1.28627 -0.654713 1.676396 -0.390548 6.96131e-01 7.86589e-01
#> gene197 591.21368 3.285941 0.278768 11.787369 4.53489e-32 4.53489e-30
#> gene198 4.67660 2.434828 0.961683 2.531839 1.13466e-02 2.33951e-02
#> gene199 14.96302 -2.313151 0.491582 -4.705521 2.53218e-06 1.17776e-05
#> gene200 17.69265 1.970386 0.602859 3.268401 1.08157e-03 3.00436e-03
tr_clean_deseq2_result(ex_deseq_results, p_adjusted = 0.1, fold_change = 2)
#> Found 110 DE genes for condition B vs A.
#> # A tibble: 110 × 7
#> gene baseMean log2FoldChange lfcSE stat pvalue padj
#> <chr> <dbl> <dbl> <dbl> <dbl> <dbl> <dbl>
#> 1 gene95 853. 3.35 0.279 12.0 3.26e-33 6.53e-31
#> 2 gene197 591. 3.29 0.279 11.8 4.53e-32 4.53e-30
#> 3 gene180 420. 3.30 0.298 11.1 1.57e-28 1.05e-26
#> 4 gene70 235. -2.91 0.276 -10.5 5.23e-26 2.62e-24
#> 5 gene106 886. 3.08 0.303 10.1 3.80e-24 1.52e-22
#> 6 gene187 57.3 -4.28 0.428 -10.0 1.42e-23 4.74e-22
#> 7 gene26 93.9 4.62 0.473 9.77 1.47e-22 4.20e-21
#> 8 gene68 72.7 -3.23 0.345 -9.37 7.58e-21 1.90e-19
#> 9 gene122 462. 2.63 0.307 8.58 9.79e-18 2.18e-16
#> 10 gene39 191. 2.67 0.325 8.20 2.33e-16 4.66e-15
#> # ℹ 100 more rows
tr_theme
#> R version 4.3.2 (2023-10-31)
#> Platform: x86_64-pc-linux-gnu (64-bit)
#> Running under: Ubuntu 22.04.3 LTS
#>
#> Matrix products: default
#> BLAS: /usr/lib/x86_64-linux-gnu/openblas-pthread/libblas.so.3
#> LAPACK: /usr/lib/x86_64-linux-gnu/openblas-pthread/libopenblasp-r0.3.20.so; LAPACK version 3.10.0
#>
#> locale:
#> [1] LC_CTYPE=C.UTF-8 LC_NUMERIC=C LC_TIME=C.UTF-8
#> [4] LC_COLLATE=C.UTF-8 LC_MONETARY=C.UTF-8 LC_MESSAGES=C.UTF-8
#> [7] LC_PAPER=C.UTF-8 LC_NAME=C LC_ADDRESS=C
#> [10] LC_TELEPHONE=C LC_MEASUREMENT=C.UTF-8 LC_IDENTIFICATION=C
#>
#> time zone: UTC
#> tzcode source: system (glibc)
#>
#> attached base packages:
#> [1] stats4 stats graphics grDevices utils datasets methods
#> [8] base
#>
#> other attached packages:
#> [1] ggplot2_3.4.4 DESeq2_1.40.2
#> [3] SummarizedExperiment_1.30.2 Biobase_2.60.0
#> [5] MatrixGenerics_1.12.3 matrixStats_1.1.0
#> [7] GenomicRanges_1.52.1 GenomeInfoDb_1.36.4
#> [9] IRanges_2.34.1 S4Vectors_0.38.2
#> [11] BiocGenerics_0.46.0 tRavis_0.73.20
#>
#> loaded via a namespace (and not attached):
#> [1] tidyselect_1.2.0 viridisLite_0.4.2 dplyr_1.1.4
#> [4] farver_2.1.1 bitops_1.0-7 fastmap_1.1.1
#> [7] lazyeval_0.2.2 RCurl_1.98-1.13 janitor_2.2.0
#> [10] digest_0.6.33 timechange_0.2.0 lifecycle_1.0.4
#> [13] magrittr_2.0.3 compiler_4.3.2 rlang_1.1.2
#> [16] sass_0.4.7 tools_4.3.2 utf8_1.2.4
#> [19] yaml_2.3.7 data.table_1.14.8 knitr_1.45
#> [22] S4Arrays_1.0.6 labeling_0.4.3 htmlwidgets_1.6.2
#> [25] DelayedArray_0.26.7 abind_1.4-5 BiocParallel_1.34.2
#> [28] withr_2.5.2 purrr_1.0.2 desc_1.4.2
#> [31] grid_4.3.2 fansi_1.0.5 colorspace_2.1-0
#> [34] scales_1.2.1 cli_3.6.1 rmarkdown_2.25
#> [37] crayon_1.5.2 ragg_1.2.6 generics_0.1.3
#> [40] httr_1.4.7 tzdb_0.4.0 rjson_0.2.21
#> [43] cachem_1.0.8 stringr_1.5.1 zlibbioc_1.46.0
#> [46] parallel_4.3.2 XVector_0.40.0 vctrs_0.6.4
#> [49] Matrix_1.6-1.1 jsonlite_1.8.7 hms_1.1.3
#> [52] systemfonts_1.0.5 locfit_1.5-9.8 plotly_4.10.3
#> [55] tidyr_1.3.0 jquerylib_0.1.4 glue_1.6.2
#> [58] pkgdown_2.0.7 codetools_0.2-19 lubridate_1.9.3
#> [61] stringi_1.8.1 gtable_0.3.4 munsell_0.5.0
#> [64] tibble_3.2.1 pillar_1.9.0 htmltools_0.5.7
#> [67] GenomeInfoDbData_1.2.10 R6_2.5.1 textshaping_0.3.7
#> [70] rprojroot_2.0.4 evaluate_0.23 lattice_0.21-9
#> [73] readr_2.1.4 highr_0.10 memoise_2.0.1
#> [76] snakecase_0.11.1 bslib_0.5.1 Rcpp_1.0.11
#> [79] xfun_0.41 fs_1.6.3 pkgconfig_2.0.3