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PRESCOTT
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Cycle Analytics
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Mustafa Tekpinar
PRESCOTT
Commits
5647766c
Commit
5647766c
authored
Mar 30, 2023
by
Mustafa Tekpinar
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The program won't write *_pred_evolEpi.txt and *_pred_evolInd.txt files anymore.
parent
f5de1a26
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computePred.R
computePred.R
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computePred.R
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5647766c
...
@@ -129,7 +129,7 @@ predInd = computePredNbSeqs(wt,nbSeqs)
...
@@ -129,7 +129,7 @@ predInd = computePredNbSeqs(wt,nbSeqs)
rownames
(
predInd
)
=
aa
rownames
(
predInd
)
=
aa
# output the sequence counts log-odd ratios
# output the sequence counts log-odd ratios
write.table
(
predInd
,
paste0
(
prot
,
"_pred_evolInd.txt"
))
#
write.table(predInd,paste0(prot,"_pred_evolInd.txt"))
print
(
"done"
)
print
(
"done"
)
print
(
"running global epistatic model..."
)
print
(
"running global epistatic model..."
)
...
@@ -139,7 +139,7 @@ rownames(pred)=aa
...
@@ -139,7 +139,7 @@ rownames(pred)=aa
# output the evolutionary distances between the query and the closest variants
# output the evolutionary distances between the query and the closest variants
evolDist
=
pred
/
sum
(
trace
^
2
)
evolDist
=
pred
/
sum
(
trace
^
2
)
evolDist
[
is.na
(
evolDist
)]
=
1
evolDist
[
is.na
(
evolDist
)]
=
1
write.table
(
evolDist
,
paste0
(
prot
,
"_pred_evolEpi.txt"
))
#
write.table(evolDist,paste0(prot,"_pred_evolEpi.txt"))
print
(
"done"
)
print
(
"done"
)
print
(
"running normalization..."
)
print
(
"running normalization..."
)
...
...
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