Commit 606b4597 by Mustafa Tekpinar

Changed the default value for the wild type (namely, NA values) from 0.0 to 2.0.

parent bd075e8c
......@@ -146,7 +146,7 @@ def parseGEMMEoutput(inputFile, verbose):
if item[0] == "\"":
aaColumn.append(item)
elif (item == 'NA'):
tempList.append(0.0000000)
tempList.append(2.0000000)
else:
tempList.append(float(item))
matrixData.append(tempList)
......
......@@ -362,7 +362,7 @@ computePredSimple<-function(mat, distTrace, wt, thresh){
if((i==694) & (a=="v")) {
print(i)
print(sel)
#print(distTrace[sel-1])
print(distTrace[sel-1])
print(sortedDist)
}
......@@ -393,6 +393,8 @@ normalizePred<-function(pred, trace, wt){
normPred[,i] = pred[,i] / max(pred[!is.na(pred)])
normPred[is.na(normPred[,i]),i] = 1
normPred[,i] = normPred[,i] * trace[i]
# If the residue is the wild type, it is replaced by NA.
# As explained above, NA corresponds to 2.
normPred[aa==wt[i],i] = NA
}
return(-normPred)
......
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