my_runsims: A version of PROPER:::runsims which is (hopefully) a little...

In elsayed-lab/hpgltools: A pile of (hopefully) useful R functions

A version of PROPER:::runsims which is (hopefully) a little more robust.

Description

When I was testing PROPER, it fell down mysteriously on a few occasions. The source ended up being in runsims(), ergo this function. This is therefore mostly a copy/paste of that function with a few small changes.

Usage

my_runsims(
  Nreps = c(3, 5, 7, 10),
  Nreps2,
  nsims = 100,
  sim.opts,
  DEmethod = c("edgeR", "DSS", "DESeq", "DESeq2"),
  verbose = TRUE
)

Arguments

Nreps	Vector of numbers of replicates to simulate.
Nreps2	Second vector of replicates.
nsims	How many simulations to perform?
sim.opts	Options provided in a list which include information about the expression, numbers of genes, logFC values, etc.
DEmethod	I suggest using only either edgeR or DESeq2.
verbose	Print some information along the way?

See Also

[PROPER]

elsayed-lab/hpgltools documentation built on May 9, 2024, 5:02 a.m.