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Laura Denies
PathoFact
Commits
96dde8eb
Commit
96dde8eb
authored
May 20, 2020
by
Laura Denies
Browse files
Update AMR_MGE.R
parent
357dd754
Changes
1
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scripts/AMR_MGE.R
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96dde8eb
...
...
@@ -76,7 +76,14 @@ VirSorter$ContigID <- sprintf("%010d", VirSorter$ContigID)
## Combine Phage prediction
Phage_prediction
<-
merge
(
VirFinder
,
VirSorter
,
by
=
"ContigID"
,
all
=
TRUE
)
Phage_prediction
$
VirSorter_prediction
<-
fct_explicit_na
(
Phage_prediction
$
VirSorter_prediction
,
na_level
=
"-"
)
#Phage_prediction$VirSorter_prediction <- fct_explicit_na(Phage_prediction$VirSorter_prediction, na_level = "-")
if
(
all
(
is.na
(
Phage_prediction
$
VirSorter_prediction
))){
# issue #39
Phage_prediction
$
VirSorter_prediction
<-
factor
(
rep
(
"-"
,
nrow
(
Phage_prediction
)))
}
else
{
Phage_prediction
$
VirSorter_prediction
<-
fct_explicit_na
(
Phage_prediction
$
VirSorter_prediction
,
na_level
=
"-"
)
}
# Combine AMR/MGE with Phage prediction
AMR_MGE
<-
merge
(
AMR_Plasmid
,
Phage_prediction
,
by
=
"ContigID"
,
all
=
TRUE
)
...
...
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