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Update VarTierDiseaseDBFalse.R #37

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Update VarTierDiseaseDBFalse.R #37

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6 changes: 2 additions & 4 deletions run/VarTierDiseaseDBFalse.R
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Original file line number Diff line number Diff line change
Expand Up @@ -212,8 +212,6 @@ VEP.f2 <- unique(VEP.f1.maxIMAPCT[,c("Uploaded_variation", "SYMBOL","Gene","GT",

# STEP 3: assign Tiers ####

# VEP.f2$GT <- ifelse(VEP.f2$GT=="HET", "0/1","1/1")

# though Tier classification is Gene based, Tier should be assigned to each Variant

VEP.Tier.part1 <- data.frame(matrix(ncol = ncol(VEP.f2) + 6, nrow = 0))
Expand All @@ -236,7 +234,7 @@ for (g in unique(VEP.f2$Gene)){

# duplicate rows with HOM var
if ("HOM" %in% g.df$GT){
g.df2 <- rbind(g.df, g.df[g.df$GT == "1/1",])
g.df2 <- rbind(g.df, g.df[g.df$GT == "HOM",])
}
IMPACT.max <- g.df2$IMPACT.max
if(sum(IMPACT.max==4) >=2){
Expand Down Expand Up @@ -334,7 +332,7 @@ for (g in unique(VEP.Tier$Gene)){

# duplicate rows with HOM var
if ("HOM" %in% g.df$GT){
g.df2 <- rbind(g.df, g.df[g.df$GT == "1/1",])
g.df2 <- rbind(g.df, g.df[g.df$GT == "HOM",])
}
IMPACT.max <- g.df2$IMPACT.max

Expand Down
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