neighbor_finder: neighbor_finder

In ilwookkim/TCGANetwork: Gene co-expression network

Description

This function allows the user to find neighbor genes network of interested gene.

Usage

neighbor_finder(
  countdata,
  gene = gene_of_interest,
  cor.cut.off = 0.39,
  weight.cut.off = 0.5
)

Arguments

countdata	RNAseq countdata
gene	string, gene of interest to find a network for.
cor.cut.off	cut off value of correlation coeffiecint to build network. Defaults to .39
weight.cut.off	cut off value of network weight to reduce edges. Defaults to .5

Value

character vector, genes that are considered neighbors of the gene of interest (including the gene of interest itself).

Examples

example.file <- system.file("extdata", "example.RData", package="cgNetwork")
load(example.file)
common_neighbor <- neighbor_finder(countdata, "CDKN1A", 0.39, 0.5)

ilwookkim/TCGANetwork documentation built on March 31, 2021, 4:03 p.m.