default_proper: Invoke PROPER and replace its default data set with data of...

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

Invoke PROPER and replace its default data set with data of interest.

Description

Recent reviewers of Najib's grants have taken an increased interest in knowing the statistical power of the various experiments. He queried Dr. Corrada-Bravo who suggested PROPER. I spent some time looking through it and, with some revervations, modified its workflow to (at least in theory) be able to examine any dataset. The workflow in question is particularly odd and warrants further discussion/analysis. This function invokes PROPER exactly as it was performed in their paper.

Usage

default_proper(
  de_tables,
  p = 0.05,
  experiment = "cheung",
  nsims = 20,
  reps = c(3, 5, 7, 10),
  de_method = "edger",
  alpha_type = "fdr",
  alpha = 0.1,
  stratify = "expr",
  target = "lfc",
  add_coverage = TRUE,
  filter = "none",
  delta = 0.5
)

Arguments

de_tables	A set of differential expression results, presumably from EdgeR or DESeq2.
p	Cutoff
experiment	The default data set in PROPER is entitled 'cheung'.
nsims	Number of simulations to perform.
reps	Simulate these number of experimental replicates.
de_method	There are a couple choices here for tools which are pretty old, my version of this only accepts deseq or edger.
alpha_type	I assume p-adjust type.
alpha	Accepted fdr rate.
stratify	There are a few options here, I don't fully understand them.
target	Cutoff.
add_coverage	Add a line showing the actual coverage observed?
filter	Apply a filter?
delta	Not epsilon! (E.g. I forget what this does).

Value

List containing the various results and plots from proper.

See Also

[PROPER] DOI:10.1093/bioinformatics/btu640

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