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COVID-19
models
Commits
4bf07ff8
Commit
4bf07ff8
authored
Apr 16, 2021
by
Marek Ostaszewski
Browse files
corrections to the function
parent
e4dcc048
Pipeline
#39943
passed with stages
in 39 seconds
Changes
2
Pipelines
1
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Integration/MINERVA_access/minerva_access_functions.R
View file @
4bf07ff8
...
...
@@ -80,11 +80,11 @@ get_annotation <- function(references, selected_type) {
}
### A function retrieving element identifiers from a given MINERVA element set
get_component_annotations
<-
function
(
components
,
annotation_type
)
{
get_component
s
_annotations
<-
function
(
components
,
annotation_type
)
{
### Get MINERVA references as a named list
message
(
paste0
(
"Retrieving "
,
annotation_type
,
"identifiers for this MINERVA collection"
))
### Apply get_annotation function
mnv_refs
<-
sapply
(
f
components
$
map_elements
,
function
(
x
)
sapply
(
x
$
references
,
get_annotation
,
annotation_type
)
)
names
(
mnv_refs
)
<-
f
components
$
models
$
name
mnv_refs
<-
sapply
(
components
$
map_elements
,
function
(
x
)
sapply
(
x
$
references
,
get_annotation
,
annotation_type
)
)
names
(
mnv_refs
)
<-
components
$
models
$
name
return
(
mnv_refs
)
}
\ No newline at end of file
Resources/Crosstalks/find_crosstalks.R
View file @
4bf07ff8
...
...
@@ -36,15 +36,6 @@ get_reactome_pathway_contents <- function(reactome_path_id) {
return
(
unlist
(
unique
(
symbols
)))
}
### A function retrieving element identifiers from MINERVA
get_mnv_refs
<-
function
(
fcomponents
)
{
### Get MINERVA HGNCs as a named list
message
(
"Retrieving MINERVA HGNCs collection"
)
mnv_refs
<-
sapply
(
fcomponents
$
map_elements
,
function
(
x
)
sapply
(
x
$
references
,
get_annotation
,
"HGNC_SYMBOL"
)
)
names
(
mnv_refs
)
<-
fcomponents
$
models
$
name
return
(
mnv_refs
)
}
### A function retrieving element identifiers from WikiPathway diagrams
get_wp_refs
<-
function
()
{
message
(
"Retrieving WP collection"
)
...
...
@@ -174,7 +165,7 @@ map_components <- get_map_components(map)
map_groups
<-
fromJSON
(
"map_groups.json"
)
### Detailed lists
mnv_refs
<-
get_
mnv_ref
s
(
map_components
)
mnv_refs
<-
get_
component_annotation
s
(
map_components
,
"HGNC_SYMBOL"
)
wp_refs
<-
get_wp_refs
()
rct_refs
<-
get_rct_refs
()
...
...
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