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eleanorsanderson committed Nov 28, 2024
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Showing 2 changed files with 263 additions and 5 deletions.
230 changes: 230 additions & 0 deletions resources/phenotypes/bmi-z-who-2007.csv
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Original file line number Diff line number Diff line change
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38 changes: 33 additions & 5 deletions resources/phenotypes/phenotype_functions.R
View file
Original file line number Diff line number Diff line change
Expand Up @@ -327,9 +327,9 @@ organise_phenotype <- function(phecode, phenotypes, df, gen_covs, covdat, agebin
}

if(phecode == "pp") {
type <- cont
type <- "cont"
cs <- list()
phecode1 <- sbp
phecode1 <- "sbp"
phen1 <- read_phenotype_data(phecode1, Sys.getenv("phenotype_input_dir"), agebins)
if(is.null(phen1)) {
return(NULL)
Expand All @@ -338,19 +338,25 @@ organise_phenotype <- function(phecode, phenotypes, df, gen_covs, covdat, agebin
phen1$value <- phen1$value + (15 * phen1$bp_med)
phen1$value <- remove_outliers(dat, phecode1)

phecode2 <- dbp
phecode2 <- "dbp"
phen2 <- read_phenotype_data(phecode2, Sys.getenv("phenotype_input_dir"), agebins)
if(is.null(phen2)) {
return(NULL)
}
phen2 <- rename(phen2, dbp = value)
phen2$value <- phen2$value + (10 * phen2$bp_med)
phen2$value <- remove_outliers(dat, phecode2)



phen <- inner_join(phen1, phen2)
phen$value <- sbp - dbp
phen <- phen %>%
select(!c(sbp, dbp))

outliers <- phen %>%
filter(!between(phen$value, -5, 5)) %>%
select('value')

}

if(phecode=="bmiz"){
Expand All @@ -376,9 +382,14 @@ organise_phenotype <- function(phecode, phenotypes, df, gen_covs, covdat, agebin
mutate(bmiz = case_when(sex==1 ~ bmiz_boys, sex==2 ~ bmiz_girls))

phen <- phen %>%
select(FID, IID, age, bmiz) %>%
select(FID, IID, age, bmiz, agebin, lsbin) %>%
rename(value = bmiz)


outliers <- phen %>%
filter(!between(phen$value, -5, 5)) %>%
select('value')

phen <- phen %>%
filter(between(phen$value, -5, 5))

Expand Down Expand Up @@ -562,7 +573,15 @@ organise_phenotype <- function(phecode, phenotypes, df, gen_covs, covdat, agebin

write.table(subset(pheno_out, select=c("FID", "IID", "value")), file=file.path(Sys.getenv("phenotype_processed_dir"), paste0(phecode, "_", age_group, "_", sex_out, ".phen")), row=FALSE, col=FALSE, qu=FALSE)

if(phecode != "pp" & phecode != "bmiz"){
cov_ids <- subset(df, pheno_id == phecode)$covs %>% strsplit(., ":") %>% {.[[1]]}
}
if(phecode == "pp"){
cov_ids <- "sex"
}
if(phecode == "bmiz"){
cov_ids <- "sex"
}
covs <- dat %>% select(all_of(c(names(gen_covs), cov_ids))) %>% filter(IID %in% pheno_out$IID) %>% filter(!duplicated(paste(FID, IID)))

write.table(covs, file=file.path(Sys.getenv("phenotype_processed_dir"), paste0(phecode, "_", age_group, "_", sex_out, ".covs")), row=FALSE, col=FALSE, qu=FALSE)
Expand Down Expand Up @@ -644,9 +663,18 @@ organise_phenotype <- function(phecode, phenotypes, df, gen_covs, covdat, agebin
sex_out = "both"
}


write.table(subset(pheno_out, select=c("FID", "IID", "value")), file=file.path(Sys.getenv("phenotype_processed_dir"), paste0(phecode, "_", age_group, "_", sex_out, ".phen")), row=FALSE, col=FALSE, qu=FALSE)

if(phecode != "pp" & phecode != "bmiz"){
cov_ids <- subset(df, pheno_id == phecode)$covs %>% strsplit(., ":") %>% {.[[1]]}
}
if(phecode == "pp"){
cov_ids <- "sex"
}
if(phecode == "bmiz"){
cov_ids <- "sex"
}
covs <- dat %>% select(all_of(c(names(gen_covs), cov_ids, "age"))) %>% filter(IID %in% pheno_out$IID) %>% filter(!duplicated(paste(FID, IID)))

write.table(covs, file=file.path(Sys.getenv("phenotype_processed_dir"), paste0(phecode, "_", age_group, "_", sex_out, ".covs")), row=FALSE, col=FALSE, qu=FALSE)
Expand Down

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