analysis_ExprNet: Computing and testing AT1 and AT2, and plotting sub-network

In ExprNet: Characterizing Differential Expression of Selected Edges on a Network

Computing and testing AT1 and AT2, and plotting sub-network

Description

Computing and testing AT1 and AT2, and plotting sub-network

Usage

analysis_ExprNet(
  data_type1,
  data_type2,
  network,
  vertex_idx_selected = NULL,
  edge_pair_selected = NULL,
  alpha_t_test = 0.05,
  AT2_perm_test = TRUE,
  num_perm = 500,
  num_cores = parallel::detectCores(),
  type1_name = "Type1",
  type2_name = "Type2",
  subnet_label = "subnet",
  plot_subnet = TRUE,
  save_edge_res = FALSE,
  save_plot = FALSE,
  save_dir = here::here(),
  ...
)

Arguments

data_type1	data.frame for phenotype 1. Each row corresponds to a vertex feature. Each column corresponds to a sample. The first column are the numeric vertex indices.
data_type2	data.frame for phenotype 2, in the same format as data_type1.
network	An igraph-package graph object. It will be converted to an undirected graph by default.
vertex_idx_selected	A numeric vector of vertex indices that you want to include in the sub-network. All edges on the network between these vertices will be included.
edge_pair_selected	A character vector of edges that you want to include in the sub-network, each element in the form "vertex1-vertex2" (e.g. "1-3").
alpha_t_test	Significance level of the t test for each edge. It does not affect the computation of AT1 and AT2.
AT2_perm_test	Logical. Whether to conduct permutation test for AT2. If FALSE, then p-value of AT2 will be returned as NA.
num_perm	Number of permutations in the permutation test.
num_cores	Number of cores to register for parallel computing in permutation test. Should be no larger than the number of available cores on the computer.
type1_name	The name for phenotype 1, used for naming files of the results.
type2_name	The name for phenotype 2.
subnet_label	A label for the sub-network, used for naming the files and setting the title in the plot.
plot_subnet	Logical. Whether to plot the sub-network.
save_edge_res	Logical. Whether the results should be saved. Set to TRUE if you plan to conduct analysis on the t statistics of the edges.
save_plot	Logical. Whether to save the plot of the sub-network.
save_dir	Directory to save the results. Results are saved in a subfolder result_ExprNet will be created under the directory.
...	Parameters for plots. For example, you may specify the size for the vertices and width for the edges.

Value

The same return as compute_AT(). A list of the following:
subnet_label: label of the subnet; num_edges: number of edges in the sub-network;
vertex_idx_selected, edge_pair_selected: the sub-network selection arguments provided by you;
t_stat: t statistics of edges in the sub-network, t_stat_perc: percentiles of these t statistics among all edges in the original network;
AT1: Value of AT1; pval_AT1: p-value of AT1;
AT2: Value of AT2; pval_AT2: p-value of AT2)

Examples

library(ExprNet)
network <- network_demo
data_type1 <- data_LGG_demo
data_type2 <- data_GBM_demo
edge_pair_selected <- c("1-8", "1-15", "2-16", "3-16", "5-10",
                        "5-16", "8-11", "8-13", "8-14", "8-15", "13-15")
# compute AT's
AT_res <- analysis_ExprNet(data_type1 = data_type1, data_type2 = data_type2, network = network,
                           edge_pair_selected = edge_pair_selected,
                           AT2_perm_test = TRUE, num_perm = 250, num_cores = 2,
                           type1_name = "LGG", type2_name = "GBM",
                           subnet_label = "Demo_GO0006306_DNA_methylation(LGG-GBM)",
                           vertex.label.cex = 1, vertex.size = 10, edge.width = 7)

ExprNet documentation built on Aug. 15, 2023, 9:08 a.m.