Finalizing Part A

.~lock.lab5_expression3.docx#

@@ -1 +1 @@
-,noah,NovaArchSys,13.10.2022 15:00,file:///home/noah/.config/libreoffice/4;
+,noah,NovaArchSys,13.10.2022 16:10,file:///home/noah/.config/libreoffice/4;

Schrick-Noah_CS-6643_Lab-5.R

@@ -48,4 +48,24 @@ dim(GxS.covfilter)
 pheno.factor <- as.factor(colnames(GxS.covfilter))
 pheno.factor
 str(pheno.factor)
-levels(pheno.factor)
+levels(pheno.factor)
+
+
+#### Part A: Logistic Regression
+# make sure HC is the reference level
+pheno.factor.relevel <- relevel(pheno.factor,"HC")  
+levels(pheno.factor.relevel) 
+# also rename levels "0"/"1" from 1/2
+levels(pheno.factor.relevel)[levels(pheno.factor.relevel)=="MDD"] <- 1
+levels(pheno.factor.relevel)[levels(pheno.factor.relevel)=="HC"] <- 0
+
+# Fit logistic model of first gene to phenotype data
+gene.row <- 2
+gene.name <-rownames(GxS.covfilter)[gene.row]
+gene.expr <- GxS.covfilter[gene.row,] 
+gene.fit <- glm(pheno.factor.relevel~gene.expr, family=binomial)  
+summary(gene.fit)
+coeff.mat <- coef(summary(gene.fit))
+b0 <- coeff.mat[1,1]
+b1 <- coeff.mat[2,1]
+b1.pval <- coeff.mat[2,4]