inst/doc/SeqNet.R

In SeqNet: Generate RNA-Seq Data from Gene-Gene Association Networks

## ----include = FALSE----------------------------------------------------------
knitr::opts_chunk$set(
  collapse = TRUE,
  comment = "#>",
  fig.width = 6,
  fig.height = 5
)

## ----setup--------------------------------------------------------------------
library(SeqNet)
set.seed(12345)

## -----------------------------------------------------------------------------
nw <- random_network(p = 100, n_modules = 5)
nw

## -----------------------------------------------------------------------------
g <- plot_network(nw)

## -----------------------------------------------------------------------------
plot_modules(nw, g)

## -----------------------------------------------------------------------------
nw <- gen_partial_correlations(nw)
is_weighted(nw)

## -----------------------------------------------------------------------------
heatmap_network(nw)

## -----------------------------------------------------------------------------
x <- gen_rnaseq(n = 20, network = nw, verbose = FALSE)$x
dim(x)

## -----------------------------------------------------------------------------
x_zinb <- gen_zinb(n = 20, network = nw, verbose = FALSE)$x
dim(x_zinb)

## -----------------------------------------------------------------------------
nw_diff <- perturb_network(nw, n_hubs = 1, n_nodes = 5)
plot_network_diff(nw, nw_diff, g)

## -----------------------------------------------------------------------------
x1 <- gen_rnaseq(n = 20, network = nw, verbose = FALSE)$x
x2 <- gen_rnaseq(n = 20, network = nw_diff, verbose = FALSE)$x
genes <- colnames(x1)
plot_gene_pair(list(network_1 = x1, network_2 = x2), genes[1], genes[2])