get_stringdb: Retrieving of information from the STRING database
In InfOmics/LErNet: LErNet: characterization of lncRNAs via context-aware network expansion and enrichment analysis
Description
Usage
Arguments
Value
Examples
Description
Retrieves the PPI network form the STRING database via the STRINGdb.
STRINGdb often only associates a primary product to a gene,
thus other products are not reported.
The function also returns the proteins associated to each gene within the STRING database.
Usage
1
get_stringdb(stringdb_tax = 9606, stringdb_thr = 900)
Arguments
stringdb_tax
taxa of the species. Default human (9606)
stringdb_thr
threshold to be applied to the score on the edges of the PPI. Default threshold value 900
Value
a list
ppia two columns data.frame representing the PPI network by listing its edges.
Examples
1
2
3
4
5
library(STRINGdb)
library(igraph)
stringdb_tax = 9606
stringdb_thr = 900
ppi_network <- LErNet::get_stringdb( stringdb_tax = stringdb_tax, stringdb_thr = stringdb_thr)
InfOmics/LErNet documentation built on April 10, 2021, 4:49 p.m.
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Description Usage Arguments Value Examples
Description
Retrieves the PPI network form the STRING database via the STRINGdb. STRINGdb often only associates a primary product to a gene, thus other products are not reported. The function also returns the proteins associated to each gene within the STRING database.
Usage
1 | get_stringdb(stringdb_tax = 9606, stringdb_thr = 900)
|
Arguments
stringdb_tax |
taxa of the species. Default human (9606) |
stringdb_thr |
threshold to be applied to the score on the edges of the PPI. Default threshold value 900 |
Value
a list
ppia two columns data.frame representing the PPI network by listing its edges.
Examples
1 2 3 4 5 | library(STRINGdb)
library(igraph)
stringdb_tax = 9606
stringdb_thr = 900
ppi_network <- LErNet::get_stringdb( stringdb_tax = stringdb_tax, stringdb_thr = stringdb_thr)
|
R Package Documentation
Browse R Packages
We want your feedback!
Note that we can't provide technical support on individual packages. You should contact the package authors for that.
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