Last updated: 2021-01-21
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Knit directory: invitroOA_pilot_repository/
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| File | Version | Author | Date | Message |
|---|---|---|---|---|
| Rmd | e0e89e1 | Anthony Hung | 2021-01-21 | download annotations and finish preprocessing of bulkRNA |
| html | e0e89e1 | Anthony Hung | 2021-01-21 | download annotations and finish preprocessing of bulkRNA |
| Rmd | 28f57fa | Anthony Hung | 2021-01-19 | Add files for analysis |
This code downloads gene annotations and creates a reference table to interpret GO enrichments.
library(biomaRt)
library(dplyr)
Attaching package: 'dplyr'The following object is masked from 'package:biomaRt':
selectThe following objects are masked from 'package:stats':
filter, lagThe following objects are masked from 'package:base':
intersect, setdiff, setequal, union#load count data
counts <- readRDS("data/raw_counts_relabeled.rds")
genes <- rownames(counts)ensembl <- useMart(host = "jul2018.archive.ensembl.org/",
biomart = "ENSEMBL_MART_ENSEMBL",
dataset = "hsapiens_gene_ensembl")
# attributePages(ensembl)
# [1] "feature_page" "structure" "homologs" "sequences" "snp" "snp_somatic"
atts <- listAttributes(ensembl, page = "feature_page")
# Obtain annotation results that are one per gene
basic <- getBM(attributes = c("ensembl_gene_id",
"external_gene_name",
"chromosome_name",
"description",
"start_position",
"end_position"),
filters = "ensembl_gene_id",
values = genes,
mart = ensembl)
stopifnot(sort(genes) == sort(basic$ensembl_gene_id))
# Obtain phenotype descriptions
pheno <- getBM(attributes = c("ensembl_gene_id",
"phenotype_description"),
filters = "ensembl_gene_id",
values = genes,
mart = ensembl)
stopifnot(genes %in% unique(pheno$ensembl_gene_id))
# Obtain GO categories
go <- getBM(attributes = c("ensembl_gene_id",
"go_id",
"name_1006"),
filters = "ensembl_gene_id",
values = genes,
mart = ensembl)basic_gene <- basic %>% arrange(ensembl_gene_id)
pheno_gene <- pheno %>% group_by(ensembl_gene_id) %>%
summarize(phenotype = paste(phenotype_description, collapse = ";")) %>%
arrange(ensembl_gene_id)`summarise()` ungrouping output (override with `.groups` argument)stopifnot(basic_gene$ensembl_gene_id == pheno_gene$ensembl_gene_id)
basic_pheno <- cbind(basic_gene, pheno_gene[, "phenotype"])
go_gene <- go %>% group_by(ensembl_gene_id) %>%
summarize(go_id = paste(go_id, collapse = ";"),
go_descrip = paste(name_1006, collapse = ";")) %>%
arrange(ensembl_gene_id)`summarise()` ungrouping output (override with `.groups` argument)combined <- merge(basic_pheno, go_gene, by = "ensembl_gene_id",
sort = TRUE, all.x = TRUE)
stopifnot(sort(genes) == combined$ensembl_gene_id)write.table(combined, file.path("data/gene-annotation.txt"),
quote = FALSE, sep = "\t", row.names = FALSE)
sessionInfo()R version 3.6.3 (2020-02-29)
Platform: x86_64-apple-darwin15.6.0 (64-bit)
Running under: macOS Catalina 10.15.7
Matrix products: default
BLAS: /Library/Frameworks/R.framework/Versions/3.6/Resources/lib/libRblas.0.dylib
LAPACK: /Library/Frameworks/R.framework/Versions/3.6/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] stats graphics grDevices utils datasets methods base
other attached packages:
[1] dplyr_1.0.2 biomaRt_2.40.5
loaded via a namespace (and not attached):
[1] Rcpp_1.0.5 pillar_1.4.6 compiler_3.6.3
[4] later_1.1.0.1 git2r_0.27.1 workflowr_1.6.2
[7] prettyunits_1.1.1 progress_1.2.2 bitops_1.0-6
[10] tools_3.6.3 bit_4.0.4 digest_0.6.25
[13] memoise_1.1.0 evaluate_0.14 RSQLite_2.2.0
[16] lifecycle_0.2.0 tibble_3.0.3 pkgconfig_2.0.3
[19] rlang_0.4.7 DBI_1.1.0 rstudioapi_0.11.0-9000
[22] curl_4.3 parallel_3.6.3 yaml_2.2.1
[25] xfun_0.16 httr_1.4.2 stringr_1.4.0
[28] knitr_1.29 generics_0.0.2 hms_0.5.3
[31] IRanges_2.18.3 S4Vectors_0.22.1 fs_1.5.0
[34] vctrs_0.3.4 tidyselect_1.1.0 stats4_3.6.3
[37] rprojroot_1.3-2 bit64_4.0.5 Biobase_2.44.0
[40] glue_1.4.2 R6_2.4.1 AnnotationDbi_1.46.1
[43] XML_3.98-1.20 rmarkdown_2.3 purrr_0.3.4
[46] blob_1.2.1 magrittr_1.5 whisker_0.4
[49] BiocGenerics_0.30.0 backports_1.1.9 promises_1.1.1
[52] ellipsis_0.3.1 htmltools_0.5.0 httpuv_1.5.4
[55] stringi_1.4.6 RCurl_1.98-1.2 crayon_1.3.4