GWAS for fitness in Drosophila

Last updated: 2018-09-26

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library(dplyr)
library(readr)
library(kableExtra)

kable_table <- function(df) {
  kable(df, "html") %>%
  kable_styling() %>%
  scroll_box(height = "300px")
}

db <- DBI::dbConnect(RSQLite::SQLite(), "data/derived/annotations.sqlite3")

# Results of four univariate linear mixed models run in GEMMA:
univariate_lmm_results <- read_csv("data/derived/lmm_results_ashr.csv") %>% 
  filter(p_wald < 1e-05) %>% 
  inner_join(tbl(db, "variants") %>% select(-chr, -position) %>% collect(), by = "SNP") %>% 
  rename(Fitness_component = parameter) %>% 
  arrange(Fitness_component, p_wald) %>% select(-lfdr) 

univariate_lmm_results <- univariate_lmm_results %>%
  left_join(tbl(db, "genes") %>% 
              select(FBID, gene_name) %>% 
              filter(FBID %in% univariate_lmm_results$FBID) %>% 
              collect(), by = "FBID")

univariate_lmm_results <- univariate_lmm_results[,c(1:10, 16, 11:15)]

# Results of one multivariate linear mixed model run in GEMMA:
multivariate_lmm_results <- read_tsv("data/derived/output/all_four_traits.assoc.txt") %>%
  filter(p_wald < 1e-05) %>% 
  inner_join(tbl(db, "variants") %>% select(-chr, -position) %>% collect(), by = "SNP") %>% 
  arrange(p_wald) %>% 
  select(-contains("Vbeta"))

multivariate_lmm_results <- multivariate_lmm_results %>%
  left_join(tbl(db, "genes") %>% 
              select(FBID, gene_name) %>% 
              filter(FBID %in% multivariate_lmm_results$FBID) %>% 
              collect(), by = "FBID")

multivariate_lmm_results <- multivariate_lmm_results[,c(1:8, 14, 9:13)]

univariate_lmm_results %>%
  filter(Fitness_component == "female_early") %>% select(-Fitness_component) %>%
  kable_table()

univariate_lmm_results %>%
  filter(Fitness_component == "female_late") %>% select(-Fitness_component) %>%
  kable_table()

univariate_lmm_results %>%
  filter(Fitness_component == "male_early") %>% select(-Fitness_component) %>%
  kable_table()

univariate_lmm_results %>%
  filter(Fitness_component == "male_late") %>% select(-Fitness_component) %>%
  kable_table()

multivariate_lmm_results %>%
  kable_table()