Simulate and select null distributions on empirical gene-gene correlations

Source: R/pcn.R

Using a principal component constructed from the sample space, we simulate null distributions with univariate Normal distributions using pcn_simulate. Then a subset of these distributions is chosen using pcn_select.

pcn_simulate(data, n.sim = 50)

pcn_select(data.sim, cl, type = c("rep", "range"), int = 5)

Arguments

data

data matrix with rows as samples, columns as features

n.sim

The number of simulated datasets to simulate

data.sim

an object from pcn_simulate

cl

vector of cluster memberships

type

select either the representative dataset ("rep") or a range of datasets ("range")

int

every int data sets from median-ranked data.sim are taken. Defaults to 5.

Value

pcn_simulate returns a list of length n.sim. Each element is a simulated matrix using this "Principal Component Normal" (pcn) procedure. pcn_select returns a list with elements

  • ranks: When type = "range", ranks of each extracted dataset shown

  • ind: index of representative simulation

  • dat: simulation data representation of all in pcNormal

Author

Derek Chiu

Examples

set.seed(9)
A <- matrix(rnorm(300), nrow = 20)
pc.dat <- pcn_simulate(A, n.sim = 50)
cl <- sample(1:4, 20, replace = TRUE)
pc.select <- pcn_select(pc.dat, cl, "rep")