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--- keller_and_evans_lab:gscan_db_ga_p [2017/01/05 18:29]
hannah_young /* Jackson Heart Study */
+++ keller_and_evans_lab:gscan_db_ga_p [2017/02/13 16:18]
scott /* Phenotypes */
@@ Line 1021: / Line 1021: @@
-== BEAGESS ==
-===Phenotypes===
+====== BEAGESS ======
+===== Phenotypes =====
 beagess_data <- read.table("/work/KellerLab/GSCAN/dbGaP/Barretts/PhenoGenotypeFiles/RootStudyConsentSet_phs000869.BEAGESS.v1.p1.c1.GRU-MDS/PhenotypeFiles/phs000869.v1.pht004610.v1.p1.c1.BEAGESS_Subject_Phenotypes.GRU-MDS.txt.gz", header=TRUE, sep="\t", stringsAsFactors=F)
@@ Line 1177: / Line 1182: @@
-===== File Paths =====
+===== Phenotypes =====
-**HMB consent phenotypes**
-/work/KellerLab/GSCAN/dbGaP/JHS/PhenoGenotypeFiles/ChildStudyConsentSet_phs000499.JHS.v3.p1.c3.HMB-IRB/PhenotypeFiles/phs000499.v3.pht003209.v1.p1.c3.J
-HS_CARe_Subject_Phenotypes.HMB-IRB.txt.gz
-**NPU consent phenotypes**
-/work/KellerLab/GSCAN/dbGaP/JHS/PhenoGenotypeFiles/ChildStudyConsentSet_phs000499.JHS.v3.p1.c1.HMB-IRB-NPU/PhenotypeFiles/phs000499.v3.pht003209.v1.p1.
-c1.JHS_CARe_Subject_Phenotypes.HMB-IRB-NPU.txt.gz
-**HMB consent genotypes**
-/work/KellerLab/GSCAN/dbGaP/JHS/PhenoGenotypeFiles/ChildStudyConsentSet_phs000499.JHS.v3.p1.c3.HMB-IRB/GenotypeFiles/phg000103.v1.JHS.genotype-cal
-ls-matrixfmt.c3.HMB-IRB/JHS_PLINK_illu_GRU.[bed/bim/fam]
-**NPU consent genotypes**
-/work/KellerLab/GSCAN/dbGaP/JHS/PhenoGenotypeFiles/ChildStudyConsentSet_phs000499.JHS.v3.p1.c1.HMB-IRB-NPU/GenotypeFiles/phg000103.v1.JHS.genotype
--calls-matrixfmt.c1.HMB-IRB-NPU/JHS_PLINK_illu_NCU.[bed/bim/fam]
-**Subject Sample Mapping File**
-/work/KellerLab/GSCAN/dbGaP/JHS/PhenoGenotypeFiles/ChildStudyConsentSet_phs000499.JHS.v3.p1.c3.HMB-IRB/GenotypeFiles/phg000104.v1.JHS.sample-info.M
-ULTI/JHS_subject_sample_map_8_10_2010.txt
-===== Phenotypes =====
@@ Line 1232: / Line 1209: @@
 names(covariates) [2] <- "iid"
 names(covariates) [6] <- "age"
+###--------------------###
+### Smoking initiation ###
+###--------------------###
+###
+### JHSCare variables are "current_smoker_baseline" and "former_smoking_baseline"
+###       current_smoker_baseline = Current smoking status at first participant visit
+###       former_smoker_baseline = Former smoking status at first participant visit
+###
+### Response options are
+###     0 - No
+###     1 - Yes
+###
+### table(si)
+###
+###    0    1    x
+### 1206 537  9
 current.smoker <- subset(mapped_geno_pcs, select=c("current_smoker_baseline", "SUBJID"))
@@ Line 1239: / Line 1233: @@
 for(i in 1:N){
   if(is.na(current.smoker[i,1]) | is.na(former.smoker[i,1])){
-     si[i] <- "x"
+    si[i] <- "x"
-   }
+  }
-   else if (current.smoker[i,1]  == 0 & former.smoker[i,1] == 0){
+  else if (current.smoker[i,1]  == 0 & former.smoker[i,1] == 0){
-     si[i] <- "1"
+    si[i] <- "1"
-   }
+  }
-   else if (current.smoker[i,1]  == 0 & former.smoker[i,1] == 1){
+  else if (current.smoker[i,1]  == 0 & former.smoker[i,1] == 1){
-     si[i] <- 2 ### former smokers are coded as 2
+    si[i] <- 2 ### former smokers are coded as 2
-   }
+  }
-  else if (current.smoker[i,1]  == 1 & former.smoker[i,1] == 0){
+ else if (current.smoker[i,1]  == 1 & former.smoker[i,1] == 0){
-     si[i] <- 2 ### current smokers are coded as 2
+    si[i] <- 2 ### current smokers are coded as 2
-   }
+  }
 }
 mapped_geno_pcs_phen <- cbind(si, mapped_geno_pcs)
+###--------------------###
+### Smoking Cessation ###
+###--------------------###
+###
+### JHSCare variables are "current_smoker_baseline" and "former_smoking_baseline"
+###       current_smoker_baseline = Current smoking status at first participant visit
+###       former_smoker_baseline = Former smoking status at first participant visit
+###
+### Response options are
+###     0 - No
+###     1 - Yes
+###
+### table(sc)
+###
+###    0    1    x
+### 1206 537  9
 current.smoker <- subset(mapped_geno_pcs, select=c("current_smoker_baseline", "SUBJID"))
@@ Line 1259: / Line 1272: @@
 for(i in 1:N){
   if(is.na(current.smoker[i,1]) | is.na(former.smoker[i,1])){
-     sc[i] <- "x"
+    sc[i] <- "x"
-   }
+  }
-   else if (current.smoker[i,1]  == 0 & former.smoker[i,1] == 0){
+  else if (current.smoker[i,1]  == 0 & former.smoker[i,1] == 0){
-     sc[i] <- "x"
+    sc[i] <- "x"
-   }
+  }
-   else if (current.smoker[i,1]  == 0 & former.smoker[i,1] == 1){
+  else if (current.smoker[i,1]  == 0 & former.smoker[i,1] == 1){
-     sc[i] <- 1 ### former smokers are coded as 1
+    sc[i] <- 1 ### former smokers are coded as 1
-   }
+  }
-  else if (current.smoker[i,1]  == 1 & former.smoker[i,1] == 0){
+ else if (current.smoker[i,1]  == 1 & former.smoker[i,1] == 0){
-     sc[i] <- 2 ### current smokers are coded as 2
+    sc[i] <- 2 ### current smokers are coded as 2
-   }
+  }
 }
 phenotypes <- cbind(sc, mapped_geno_pcs_phen)
@@ Line 1276: / Line 1289: @@
 names(phenotypes)[1] <- "fid"
-write.table(covariates, "<file path>", row.names=F, quote=F)
+write.table(covariates, "AFR.JHS.covariates.ped", row.names=F, quote=F)
-write.table(phenotypes, "<file path>", row.names=F, quote=F)
+write.table(phenotypes, "AFR.JHS.phenotypes.ped", row.names=F, quote=F)

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