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
Fabricio Almeida-Silva
Examples
data(filt.se)
genes <- rownames(filt.se)[1:10]
gcn <- exp2gcn(filt.se, SFTpower = 18, cor_method = "pearson")
#> ..connectivity..
#> ..matrix multiplication (system BLAS)..
#> ..normalization..
#> ..done.
neighbors <- get_neighbors(genes, gcn)
