SCZ 2018 Enrichment
shengqian
2022-05-16
Last updated: 2022-05-24
Checks: 6 1
Knit directory: cTWAS_analysis/
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Load gene sets
library(gseasusie)
library(tidyverse)
genesets <- gseasusie::load_gene_sets(c('gobp','gomf','gocc'))Load gene list
library(data.table)
library("AnnotationDbi")
library("org.Hs.eg.db")
data <- fread(file = "data/magma.genes.out")
data$entrez = mapIds(org.Hs.eg.db,
keys=data$GENE, #Column containing Ensembl gene ids
column="ENTREZID",
keytype="ENSEMBL",
multiVals="first")
data <- na.omit(data)
data$beta <- 1
data$se <- 1
data <- data[,c("GENE","entrez","P","beta","se","ZSTAT")]
colnames(data) <- c("ENSEMBL","ENTREZID","pvalue","beta","se","threshold.on")Gene Ontology Biological Process
ELBO: -8075.22
25.488 sec elapsed12.636 sec elapsed
Gene Ontology Molecular Function
ELBO: -8112.042
4.088 sec elapsed3.122 sec elapsedgseasusie::enrichment_volcano(logistic.fit, ora)
gseasusie::interactive_table(logistic.fit, ora)Gene Ontology Cellular Component
ELBO: -8523.049
5.228 sec elapsed2.048 sec elapsedgseasusie::enrichment_volcano(logistic.fit, ora)
gseasusie::interactive_table(logistic.fit, ora)
sessionInfo()R version 4.1.0 (2021-05-18)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Scientific Linux 7.4 (Nitrogen)
Matrix products: default
BLAS/LAPACK: /software/openblas-0.3.13-el7-x86_64/lib/libopenblas_haswellp-r0.3.13.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] stats4 stats graphics grDevices utils datasets methods
[8] base
other attached packages:
[1] org.Hs.eg.db_3.14.0 AnnotationDbi_1.56.1 IRanges_2.28.0
[4] S4Vectors_0.32.3 Biobase_2.54.0 BiocGenerics_0.40.0
[7] data.table_1.14.0 forcats_0.5.1 stringr_1.4.0
[10] dplyr_1.0.9 purrr_0.3.4 readr_2.1.2
[13] tidyr_1.2.0 tibble_3.1.7 ggplot2_3.3.6
[16] tidyverse_1.3.1 gseasusie_0.0.0.9000 workflowr_1.7.0
loaded via a namespace (and not attached):
[1] colorspace_2.0-3 ellipsis_0.3.2 rprojroot_2.0.3
[4] XVector_0.34.0 fs_1.5.0 rstudioapi_0.13
[7] farver_2.1.0 bit64_4.0.5 mvtnorm_1.1-3
[10] fansi_1.0.3 lubridate_1.7.10 xml2_1.3.2
[13] codetools_0.2-18 doParallel_1.0.17 cachem_1.0.5
[16] knitr_1.33 jsonlite_1.8.0 apcluster_1.4.9
[19] WebGestaltR_0.4.4 broom_0.7.8 dbplyr_2.1.1
[22] png_0.1-7 data.tree_1.0.0 compiler_4.1.0
[25] httr_1.4.3 tictoc_1.0.1 backports_1.2.1
[28] assertthat_0.2.1 Matrix_1.3-3 fastmap_1.1.0
[31] cli_3.3.0 later_1.2.0 htmltools_0.5.1.1
[34] tools_4.1.0 igraph_1.3.1 gtable_0.3.0
[37] glue_1.6.2 GenomeInfoDbData_1.2.7 doRNG_1.8.2
[40] Rcpp_1.0.8.3 mr.ash.alpha_0.1-42 cellranger_1.1.0
[43] jquerylib_0.1.4 vctrs_0.4.1 Biostrings_2.62.0
[46] svglite_2.1.0 crosstalk_1.1.1 iterators_1.0.14
[49] xfun_0.24 ps_1.6.0 rvest_1.0.0
[52] irlba_2.3.5 lifecycle_1.0.1 rngtools_1.5.2
[55] zlibbioc_1.40.0 getPass_0.2-2 scales_1.2.0
[58] vroom_1.5.7 spatstat.utils_2.3-1 hms_1.1.1
[61] promises_1.2.0.1 parallel_4.1.0 susieR_0.11.92
[64] emulator_1.2-21 yaml_2.2.1 curl_4.3.2
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[97] mixsqp_0.3-43 KEGGREST_1.34.0 RCurl_1.98-1.5
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[103] utf8_1.2.2 tzdb_0.3.0 rmarkdown_2.9
[106] grid_4.1.0 readxl_1.4.0 reactR_0.4.4
[109] blob_1.2.1 callr_3.7.0 git2r_0.28.0
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