There is a known gender difference in the age of schizophrenia onset. It is clearly visible in FinnGen data as well. The following R code will produce a tornado plot visualizing this difference in FinnGen population.
# get FINNGENID and the age at first schizophrenia diagnose
sql<-paste0(
"SELECT FINNGENID, MIN(AGE) AS ENTRY_AGE ",
"FROM finngen_r10_service_sector_detailed_longitudinal_v2.",
"sandbox_tools_r10.",
"finngen_r10_endpoint_cohorts_v1 ",
"WHERE ENDPOINT = 'F5_SCHZPHR' ",
"GROUP BY FINNGENID "
)
tb <- bq_project_query(projectid, sql)
df <- bq_table_download(tb)
# get the gender from baseline
df <- left_join(df, df_baseline, by = "FINNGENID")
df <- df %>%
mutate(AGE = round(ENTRY_AGE)) %>%
mutate(AGE = cut(AGE, breaks = seq(from = 0, to = 110, by = 5))) %>%
select(FINNGENID, AGE, SEX) %>%
group_by(AGE,SEX) %>%
summarise(N = n(), .groups = "drop") %>%
mutate(AGE = fct_drop(AGE)) %>%
drop_na(AGE,SEX) %>%
complete(AGE, SEX, fill = list(N = 0)) %>%
group_by(SEX) %>%
mutate(ALL = sum(N)) %>%
ungroup() %>%
mutate(PR = round(100 * N/ALL, 3)) %>%
mutate(PR = ifelse(SEX == 'female', PR, -PR))
ggplot(df, aes(x = PR, y = AGE, fill = SEX)) +
geom_bar(data = subset(df, SEX == 'female'), stat = "identity") +
geom_bar(data = subset(df, SEX == 'male'), stat = "identity")+
scale_x_continuous(labels = abs, limits = c(-15,15)) +
theme_bw() +
labs(
title = "Schizophrenia age of onset",
x = "Percentage",
y = "Age group",
fill = "Gender"
)
Location of the script's in the Sandbox
Below is a path to the R Markdown file in Sandbox. This R Markdown file can be converted to an html page using "knit" command. The R Markdown is a plain text file, so you can copy code snippets that you need.
