Updates to include pp

MRCIEU · Dec 3, 2024 · cf1dcbb · cf1dcbb
1 parent 2192fa7
commit cf1dcbb
Show file tree

Hide file tree

Showing 2 changed files with 41 additions and 33 deletions.
diff --git a/phenotype_list.csv b/phenotype_list.csv
@@ -1,24 +1,24 @@
-Name,pheno_id,var_type,units,min,max,covs,transformation,standardisation,opengwasid
-Body mass index,bmi,cont,kg/m2,0,60,sex,log,yes,ukb-b-19953
-Height,height,cont,cm,10,250,sex,none,yes,ebi-a-GCST90029008
-Waist circumference,wc,cont,cm,0,250,sex,none,yes,ukb-b-9405
-Waist to hip ratio,whr,cont,ratio,0,20,sex,none,yes,ebi-a-GCST90029009
-Total body bone mineral density,tb-bmd,cont,g/cm2,0,20,sex,none,yes,ebi-a-GCST004772
-Forced expiratory volume in 1 second,fev1,cont,l,0,10,sex,none,yes,ukb-b-19657
-FEV1/FVC ratio,fev1fvc,cont,l,0,10,sex,none,yes,ebi-a-GCST90029026
-Systolic blood pressure,sbp,cont,mmHg,0,250,sex:bp_medication,none,yes,ukb-b-20175
-Diastolic blood pressure,dbp,cont,mmHg,0,250,sex:bp_medication,none,yes,
-LDL cholesterol,ldl,cont,mmol/L,0,10,sex:cholesterol_med,none,yes,ieu-b-110
-HDL cholesterol,hdl,cont,mmol/L,0,10,sex,none,yes,ieu-b-109
-Triglycerides,trig,cont,mmol/L,0,20,sex,none,yes,ieu-b-111
-C-reactive protein,crp,cont,mg/L,0,100,sex,none,yes,ebi-a-GCST90014002
-Interleukin 6,il6,cont,pg/ml,0,100,sex,none,yes,ebi-a-GCST90012005
-Leptin,leptin,cont,ng/ml,0,100,sex,none,yes,ebi-a-GCST90007307
-Glycated haemoglobin,hba1c,cont,mmol/mol,0,70,sex,none,yes,ebi-a-GCST90014006
-Insulin,insulin,cont,pmol/L,0,200,sex,none,yes,ukb-b-15445
-Adiponectin,adiponectin,cont,ug/ml,0,100,sex,none,yes,ieu-a-1
-Calcium,calcium,cont,mmol/L,0,10,sex,none,yes,ebi-a-GCST90013999
-Vitamin D,vitd,cont,nmol/L,0,400,sex,none,yes,ebi-a-GCST90000618
-Estradiol,estradiol,cont,pmol/L,0,15000,sex,none,yes,ebi-a-GCST90012105
-Testosterone,testosterone,cont,nmol/L,0,60,sex,none,yes,ebi-a-GCST90012114
-Sex hormone binding globulin,shbg,cont,nmol/L,0,300,sex,none,yes,ieu-b-4870
+Name,pheno_id,var_type,units,min,max,covs,transformation,standardisation,opengwasid
+Body mass index,bmi,cont,kg/m2,0,60,sex,log,yes,ukb-b-19953
+Height,height,cont,cm,10,250,sex,none,yes,ebi-a-GCST90029008
+Waist circumference,wc,cont,cm,0,250,sex,none,yes,ukb-b-9405
+Waist to hip ratio,whr,cont,ratio,0,20,sex,none,yes,ebi-a-GCST90029009
+Total body bone mineral density,tb-bmd,cont,g/cm2,0,20,sex,none,yes,ebi-a-GCST004772
+Forced expiratory volume in 1 second,fev1,cont,l,0,10,sex,none,yes,ukb-b-19657
+FEV1/FVC ratio,fev1fvc,cont,l,0,10,sex,none,yes,ebi-a-GCST90029026
+Systolic blood pressure,sbp,cont,mmHg,0,250,sex:bp_med,none,yes,ukb-b-20175
+Diastolic blood pressure,dbp,cont,mmHg,0,250,sex:bp_med,none,yes,
+LDL cholesterol,ldl,cont,mmol/L,0,10,sex:cholesterol_med,none,yes,ieu-b-110
+HDL cholesterol,hdl,cont,mmol/L,0,10,sex,none,yes,ieu-b-109
+Triglycerides,trig,cont,mmol/L,0,20,sex,none,yes,ieu-b-111
+C-reactive protein,crp,cont,mg/L,0,100,sex,none,yes,ebi-a-GCST90014002
+Interleukin 6,il6,cont,pg/ml,0,100,sex,none,yes,ebi-a-GCST90012005
+Leptin,leptin,cont,ng/ml,0,100,sex,none,yes,ebi-a-GCST90007307
+Glycated haemoglobin,hba1c,cont,mmol/mol,0,70,sex,none,yes,ebi-a-GCST90014006
+Insulin,insulin,cont,pmol/L,0,200,sex,none,yes,ukb-b-15445
+Adiponectin,adiponectin,cont,ug/ml,0,100,sex,none,yes,ieu-a-1
+Calcium,calcium,cont,mmol/L,0,10,sex,none,yes,ebi-a-GCST90013999
+Vitamin D,vitd,cont,nmol/L,0,400,sex,none,yes,ebi-a-GCST90000618
+Estradiol,estradiol,cont,pmol/L,0,15000,sex,none,yes,ebi-a-GCST90012105
+Testosterone,testosterone,cont,nmol/L,0,60,sex,none,yes,ebi-a-GCST90012114
+Sex hormone binding globulin,shbg,cont,nmol/L,0,300,sex,none,yes,ieu-b-4870
diff --git a/resources/phenotypes/phenotype_functions.R b/resources/phenotypes/phenotype_functions.R
@@ -323,40 +323,48 @@ organise_phenotype <- function(phecode, phenotypes, df, gen_covs, covdat, agebin
     type <- filter(df, pheno_id == phecode)$var_type
     str(filter(df, pheno_id == phecode))
     cs <- list()
-    phen <- read_phenotype_data(phecode, Sys.getenv("phenotype_input_dir"), agebins)
+    adjust_covs <- NULL
+    if(phecode == "ldl"){
+      adjust_covs <- "cholesterol_med"
+      }
+    phen <- read_phenotype_data(phecode, Sys.getenv("phenotype_input_dir"), agebins, adjust_covs)
   }
 
   if(phecode == "pp") {
     type <- "cont"
     cs <- list()
     phecode1 <- "sbp"
-    phen1 <- read_phenotype_data(phecode1, Sys.getenv("phenotype_input_dir"), agebins)
+    phen1 <- read_phenotype_data(phecode1, Sys.getenv("phenotype_input_dir"), agebins, "bp_med")
     if(is.null(phen1)) {
       return(NULL)
     }
-    phen1 <- rename(phen1, sbp = value)
+
     phen1$value <- phen1$value + (15 * phen1$bp_med)
-    phen1$value <- remove_outliers(dat, phecode1)
+    phen1 <- remove_outliers(phen1, phecode1)
+    phen1 <- rename(phen1, sbp = value)
 
     phecode2 <- "dbp"
-    phen2 <- read_phenotype_data(phecode2, Sys.getenv("phenotype_input_dir"), agebins)
+    phen2 <- read_phenotype_data(phecode2, Sys.getenv("phenotype_input_dir"), agebins, "bp_med")
     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)
 
+    phen2$value <- phen2$value + (10 * phen2$bp_med)
+    phen2 <- remove_outliers(phen2, phecode2)
+    phen2 <- rename(phen2, dbp = value)
 
     phen <- inner_join(phen1, phen2)
-    phen$value <- sbp - dbp
+    phen$value <- phen$sbp - phen$dbp
     phen <- phen %>%
       select(!c(sbp, dbp))
 
     outliers <-  phen %>% 
       filter(!between(phen$value, 10, 180)) %>% 
       select('value')
 
+    phen <- phen %>%
+      filter(between(phen$value, 10, 180))
+
   }
 
   if(phecode=="bmiz"){