library(syntenet)
library(doubletrouble)
library(here)
library(tidyverse)
library(BiocParallel)
set.seed(123) # for reproducibility
options(timeout = 1e10) # to allow download of big files
# Load helper functions
source(here("code", "utils.R"))3 Calculating substitution rates for selected Ensembl genomes
Here, we will describe the code to calculate substitution rates for selected genomes in Ensembl and Ensembl Genomes instances using the Bioconductor package doubletrouble.
3.1 Data loading
Here, we will load the data frames of species metadata and the lists of duplicated gene pairs for each Ensembl instance.
# Load metadata
load(here("products", "result_files", "metadata_all.rda"))
# Load duplicates
load(here("products", "result_files", "fungi_duplicates.rda"))
load(here("products", "result_files", "plants_duplicates.rda"))3.2 Calculating substitution rates
Next, we will calculate substitution rates (\(K_a\), \(K_s\), and \(K_a/K_s\)) for duplicate pairs in all selected species, namely:
Three fungi species (Saccharomyces cerevisiae, Candida glabrata, and Schizosaccharomyces pombe).
Four legume species (Glycine max, Phaseolus vulgaris, Vitis vinifera, Selaginella moellendorffii).
# Fungi - S. cerevisiae, Candida glabrata, and Schizosaccharomyces pombe
## Download CDS
selected_fungi <- c(
"saccharomyces_cerevisiae", "candida_glabrata", "schizosaccharomyces_pombe"
)
fungi_cds <- get_cds_ensembl(selected_fungi, ensembl = "fungi")
## Calculate substitution rates
fungi_kaks <- pairs2kaks(
gene_pairs_list = fungi_duplicates[selected_fungi],
cds = fungi_cds,
bp_param = BiocParallel::SnowParam(workers = 8)
)
# Plants - Glycine max, Phaseolus vulgaris, Vitis vinifera, and Selaginella moellendorffii
## Download CDS
selected_plants <- c(
"glycine_max", "phaseolus_vulgaris", "vitis_vinifera",
"selaginella_moellendorffii"
)
plants_cds <- get_cds_ensembl(selected_plants, ensembl = "plants")
## Calculate substitution rates
plants_duplicates <- plants_duplicates[selected_plants]
plants_kaks <- pairs2kaks(
gene_pairs_list = plants_duplicates,
cds = plants_cds,
bp_param = BiocParallel::SnowParam(workers = 8)
)Saving objects as .rda files:
save(
fungi_kaks, compress = "xz",
file = here("products", "result_files", "fungi_kaks.rda")
)
save(
plants_kaks, compress = "xz",
file = here("products", "result_files", "plants_kaks.rda")
)Session info
This document was created under the following conditions:
─ Session info ───────────────────────────────────────────────────────────────
setting value
version R version 4.3.2 (2023-10-31)
os Ubuntu 22.04.3 LTS
system x86_64, linux-gnu
ui X11
language (EN)
collate en_US.UTF-8
ctype en_US.UTF-8
tz Europe/Brussels
date 2024-02-27
pandoc 3.1.1 @ /usr/lib/rstudio/resources/app/bin/quarto/bin/tools/ (via rmarkdown)
─ Packages ───────────────────────────────────────────────────────────────────
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