cgNetwork: cgNetwork

In ilwookkim/TCGANetwork: Gene co-expression network

Description

Find gene networks around gene of interest, one for WT and one for mutated.

Usage

cgNetwork(
  countdata,
  mut_df,
  common_neighbor,
  cor_method = "spearman",
  weight.cut.off = 0.5
)

Arguments

countdata,	output of the cgData or TCGA_RNAseq_RSEM function.
mut_df	data.frame, output of the cgMutation or mutation_info function.
common_neighbor	character vector, names of genes considered neighbors of the gene of interest. Output of the neighbor_finder function.
cor_method	string, correlation coeffiecint method "spearman" or "pearson". Defaults to "spearman".
weight.cut.off	numeric, cut off value of network weight to reduce edges. Defaults to 0.5.

Value

list of two igraph objects

Examples

example.file <- system.file("extdata", "example.RData", package="cgNetwork")
load(example.file)
cgNetwork_list <- cgNetwork(countdata, mut_df, common_neighbor, "spearman", 0.5)

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