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I performed gene enrichment analysis using GO.db. It gave me back some GOs with up and down genes but it doesn't say what those genes are. Any idea how to do that? I didn't have any problem with the code, I just don't know what to do after that. This is what I have done so far
qlf<- glmQLFTest(fit, contrast = contr.matrix[,10])
go <- goana(qlf, species = "Mm")
topGO_2000 <- topGO(go, n=2000, truncate=2000)
topGO_2000 <-topGO_2000 %>%
filter( P.Up < 0.001 | P.Down < 0.001)
sessionInfo()
R version 4.0.2 (2020-06-22)
Platform: x86_64-apple-darwin17.0 (64-bit)
Running under: macOS Catalina 10.15.7
Matrix products: default
BLAS: /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib
LAPACK: /Library/Frameworks/R.framework/Versions/4.0/Resources/lib/libRlapack.dylib
locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
attached base packages:
[1] grid stats4 parallel stats graphics grDevices utils datasets methods base
other attached packages:
[1] Rgraphviz_2.34.0 topGO_2.42.0 SparseM_1.81 graph_1.68.0 org.Mm.eg.db_3.12.0
[6] GO.db_3.12.1 AnnotationDbi_1.52.0 IRanges_2.24.1 S4Vectors_0.28.1 biomaRt_2.46.3
[11] forcats_0.5.1 stringr_1.4.0 dplyr_1.0.5 purrr_0.3.4 readr_1.4.0
[16] tidyr_1.1.3 tibble_3.1.1 ggplot2_3.3.3 tidyverse_1.3.1 RColorBrewer_1.1-2
[21] RTN_2.15.2 edgeR_3.32.1 limma_3.46.0 Biobase_2.50.0 BiocGenerics_0.36.1
loaded via a namespace (and not attached):
[1] colorspace_2.0-0 ellipsis_0.3.1 class_7.3-17 rio_0.5.26
[5] XVector_0.30.0 GenomicRanges_1.42.0 fs_1.5.0 rstudioapi_0.13
[9] proxy_0.4-25 bit64_4.0.5 fansi_0.4.2 lubridate_1.7.10
[13] xml2_1.3.2 splines_4.0.2 cachem_1.0.4 jsonlite_1.7.2
[17] broom_0.7.6 kernlab_0.9-29 dbplyr_2.1.1 pheatmap_1.0.12
[21] compiler_4.0.2 httr_1.4.2 backports_1.2.1 assertthat_0.2.1
[25] Matrix_1.2-18 fastmap_1.1.0 cli_2.5.0 prettyunits_1.1.1
[29] tools_4.0.2 igraph_1.2.6 gtable_0.3.0 glue_1.4.2
[33] GenomeInfoDbData_1.2.4 rappdirs_0.3.3 tinytex_0.31 Rcpp_1.0.6
[37] carData_3.0-4 cellranger_1.1.0 vctrs_0.3.7 xfun_0.22
[41] openxlsx_4.2.3 rvest_1.0.0 lifecycle_1.0.0 statmod_1.4.35
[45] XML_3.99-0.6 zlibbioc_1.36.0 MASS_7.3-51.6 scales_1.1.1
[49] minet_3.48.0 hms_1.0.0 MatrixGenerics_1.2.1 SummarizedExperiment_1.20.0
[53] pwr_1.3-0 curl_4.3 memoise_2.0.0 viper_1.24.0
[57] segmented_1.3-4 stringi_1.5.3 RSQLite_2.2.7 e1071_1.7-6
[61] zip_2.1.1 GenomeInfoDb_1.26.7 rlang_0.4.10 pkgconfig_2.0.3
[65] matrixStats_0.58.0 bitops_1.0-7 lattice_0.20-41 bit_4.0.4
[69] tidyselect_1.1.0 magrittr_2.0.1 R6_2.5.0 snow_0.4-3
[73] generics_0.1.0 DelayedArray_0.16.3 DBI_1.1.1 pillar_1.6.0
[77] haven_2.4.1 foreign_0.8-80 withr_2.4.2 mixtools_1.2.0
[81] survival_3.1-12 abind_1.4-5 RCurl_1.98-1.3 RedeR_1.38.0
[85] modelr_0.1.8 crayon_1.4.1 car_3.0-10 KernSmooth_2.23-17
[89] utf8_1.2.1 BiocFileCache_1.14.0 progress_1.2.2 locfit_1.5-9.4
[93] readxl_1.3.1 data.table_1.14.0 blob_1.2.1 reprex_2.0.0
[97] openssl_1.4.3 munsell_0.5.0 askpass_1.1
It does work, thanks. It is a bit tricky because the code is for one GO at the time but I made a loop so no big issues. Thanks