Skip to content
GitLab
Projects
Groups
Snippets
/
Help
Help
Support
Community forum
Keyboard shortcuts
?
Submit feedback
Sign in
Toggle navigation
Menu
Open sidebar
David Hoksza
bh19-rare-diseases
Commits
fc0d38d0
Commit
fc0d38d0
authored
Dec 05, 2019
by
Marek Ostaszewski
Browse files
minor updates
parent
fb98b1a6
Changes
1
Hide whitespace changes
Inline
Side-by-side
associations/extend_network/get_extended_network.R
View file @
fc0d38d0
...
...
@@ -75,11 +75,9 @@ retrieve_stringdb_net <- function(finput, fn, fscore) {
score
=
json
[[
1
]]
$
scores
$
`stringdb::score`
,
stringsAsFactors
=
F
)
ppi_network
<-
ppi_network
[
ppi_network
$
score
>=
fscore
,]
ppi_network
<-
unique
(
ppi_network
[
ppi_network
$
score
>=
fscore
,]
)
ppi_network
$
source
<-
gsub
(
'9606.'
,
""
,
ppi_network
$
source
)
ppi_network
$
target
<-
gsub
(
'9606.'
,
""
,
ppi_network
$
target
)
ppi_network
ppi_network
<-
unique
(
ppi_network
)
message
(
"after pruning by score, the network contains "
,
dim
(
ppi_network
)[
1
],
" interactions "
)
return
(
ppi_network
)
}
...
...
@@ -146,6 +144,9 @@ if (dbsource == "stringdb" | dbsource == "text_mining") {
}
}
### if PPI network is either null (no text mining requested) or empty
### fall back completely to OmniPathDB network
### else use OmniPathDB to filter out the text mining results
if
(
length
(
ppi_network
)
==
0
)
{
message
(
"No text mining network, relying only on OmniPathDB"
)
ppi_network
<-
retrieve_omnipath
(
input
)
...
...
Write
Preview
Supports
Markdown
0%
Try again
or
attach a new file
.
Cancel
You are about to add
0
people
to the discussion. Proceed with caution.
Finish editing this message first!
Cancel
Please
register
or
sign in
to comment