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APPINetwork
Commits
26173fc5
Commit
26173fc5
authored
May 10, 2022
by
Simon Gosset
Browse files
modif thesaurus col put et transp
parent
2b776d1c
Changes
2
Hide whitespace changes
Inline
Side-by-side
R/biogrid_window_opt.R
View file @
26173fc5
...
...
@@ -183,7 +183,7 @@ format_database = function(organism,organismID, putative, file, uniprot, pathrac
# eliminate putative proteins
if
(
putative
==
" TRUE"
)
{
thesaurusNotranNoPut
<-
thesaurusNotranNoPut
[
thesaurusNotranNoPut
[,
5
]
==
"FALSE"
,]
thesaurusNotranNoPut
<-
thesaurusNotranNoPut
[
thesaurusNotranNoPut
[,
5
]
==
"FALSE"
,]
Tab.putatives
<-
thesaurus
[
thesaurus
[,
5
]
==
" TRUE"
,]
Tab.putatives
[,
2
]
<-
unlist
(
apply
(
Tab.putatives
,
c
(
1
,
2
),
strsplit
,
split
=
";"
)[,
2
])
for
(
i
in
1
:
dim
(
Tab.putatives
)[
1
])
{
...
...
@@ -195,20 +195,21 @@ format_database = function(organism,organismID, putative, file, uniprot, pathrac
}
uniprotthesaurusNotranNoPut
<-
unlist
(
apply
(
thesaurusNotranNoPut
,
c
(
1
,
2
),
strsplit
,
split
=
";"
)[,
2
])
# new
biogridA
<-
irefindex
[,
1
]
biogridB
<-
irefindex
[,
2
]
prsbar
<-
txtProgressBar
(
min
=
1
,
max
=
dim
(
thesaurusNotranNoPut
)[
1
],
style
=
3
)
if
(
length
(
thesaurus_data
[
1
,])
!=
6
)
{
putative_col
=
rep
(
NA
,
length
(
thesaurus_data
[,
1
]))
thesaurus_data
=
cbind
(
thesaurus_data
,
putative_col
)
colnames
(
thesaurus_data
)[
9
]
=
"Putative"
thesaurus_data
=
cbind
(
thesaurus_data
,
putative_col
)
colnames
(
thesaurus_data
)[
10
]
=
"Transposon"
}
#
if (length(thesaurus_data[1,]) != 6) {
#
putative_col = rep(NA, length(thesaurus_data[,1]))
#
thesaurus_data = cbind(thesaurus_data, putative_col)
#
colnames(thesaurus_data)[9] = "Putative"
#
#
thesaurus_data = cbind(thesaurus_data, putative_col)
#
colnames(thesaurus_data)[10] = "Transposon"
#
}
# print(thesaurus_data[1:10,])
# print(thesaurusNotranNoPut[thesaurusNotranNoPut[,5]==" TRUE",])
...
...
@@ -239,7 +240,7 @@ format_database = function(organism,organismID, putative, file, uniprot, pathrac
irefindex
[
irefindex
[,
2
]
==
uniprotthesaurusNotranNoPut
[
i
][
u
],
4
]
<-
thesaurusNotranNoPut
[
i
,
3
]
irefindex
[
irefindex
[,
2
]
==
uniprotthesaurusNotranNoPut
[
i
][
u
],
15
]
<-
thesaurusNotranNoPut
[
i
,
4
]
irefindex
[
irefindex
[,
2
]
==
uniprotthesaurusNotranNoPut
[
i
][
u
],
2
]
<-
thesaurusNotranNoPut
[
i
,
1
]
thesaurus_data
[
!
is.na
(
thesaurus_data
[,
1
])
&
thesaurus_data
[,
1
]
==
thesaurusNotranNoPut
[
i
,
1
],
9
:
10
]
=
thesaurusNotranNoPut
[
i
,
5
:
6
]
thesaurus_data
[
!
is.na
(
thesaurus_data
[,
1
])
&
thesaurus_data
[,
1
]
==
thesaurusNotranNoPut
[
i
,
1
],
9
:
10
]
=
thesaurusNotranNoPut
[
i
,
5
:
6
]
}
setTxtProgressBar
(
prsbar
,
i
)
}
...
...
@@ -257,12 +258,12 @@ format_database = function(organism,organismID, putative, file, uniprot, pathrac
print
(
database.path
)
organism
<-
gsub
(
" "
,
"-"
,
organism
)
outfilename
<-
paste
(
organism
,
"_biogrid.txt"
,
sep
=
""
)
write.table
(
irefindex
,
file
=
outfilename
,
row.names
=
F
,
col.names
=
T
,
quote
=
F
,
sep
=
"\t"
)
write.table
(
thesaurus_data
,
file
=
sortie
,
row.names
=
F
,
col.names
=
T
,
quote
=
F
,
sep
=
"\t"
)
...
...
R/test.R
0 → 100644
View file @
26173fc5
rm
(
list
=
ls
())
library
(
appinetwork
)
source
(
"tfit.R"
)
source
(
"assembly_intermediary_window.R"
)
source
(
"intact_window.R"
)
source
(
"biogrid_window_opt.R"
)
source
(
"interface.R"
)
source
(
"thesaurus_window.R"
)
source
(
"build_network_window.R"
)
source
(
"irefindex_window.R"
)
source
(
"clustering_tfit_window.R"
)
source
(
"methods.R"
)
interface
()
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