get_neighbors: Get 1st-order neighbors of a given gene or group of genes
In almeidasilvaf/BioNERO: Biological Network Reconstruction Omnibus
View source: R/gcn_inference.R
get_neighbors R Documentation
Get 1st-order neighbors of a given gene or group of genes
Description
Get 1st-order neighbors of a given gene or group of genes
Usage
get_neighbors(genes, net, cor_threshold = 0.7)
Arguments
genes
Character vector containing genes from which
direct neighbors will be extracted.
net
List object returned by exp2gcn.
cor_threshold
Correlation threshold to filter connections.
As a weighted network is a fully connected graph, a cutoff must be selected.
Default is 0.7.
Value
List containing 1st-order neighbors for each input gene.
Author(s)
Fabricio Almeida-Silva
See Also
exp2gcn SFT_fit
Examples
data(filt.se)
genes <- rownames(filt.se)[1:10]
gcn <- exp2gcn(filt.se, SFTpower = 18, cor_method = "pearson")
neighbors <- get_neighbors(genes, gcn)
almeidasilvaf/BioNERO documentation built on Oct. 9, 2024, 1:49 a.m.
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View source: R/gcn_inference.R
| get_neighbors | R Documentation |
Get 1st-order neighbors of a given gene or group of genes
Description
Get 1st-order neighbors of a given gene or group of genes
Usage
get_neighbors(genes, net, cor_threshold = 0.7)
Arguments
genes |
Character vector containing genes from which direct neighbors will be extracted. |
net |
List object returned by |
cor_threshold |
Correlation threshold to filter connections. As a weighted network is a fully connected graph, a cutoff must be selected. Default is 0.7. |
Value
List containing 1st-order neighbors for each input gene.
Author(s)
Fabricio Almeida-Silva
See Also
exp2gcn SFT_fit
Examples
data(filt.se)
genes <- rownames(filt.se)[1:10]
gcn <- exp2gcn(filt.se, SFTpower = 18, cor_method = "pearson")
neighbors <- get_neighbors(genes, gcn)
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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