simple_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 is a modified version of 'default_proper()' above and invokes PROPER after re-formatting a given dataset in the way expected by PROPER.

Usage

simple_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",
  mean_or_median = "mean",
  filter = "none",
  delta = 1,
  add_coverage = TRUE,
  target_power = 0.8,
  mean_gene_length = 2000,
  nt_per_read = 200,
  describe_samples = 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.
mean_or_median	Use mean or median values?
filter	Apply a filter?
delta	Not epsilon! (E.g. I forget what this does).
add_coverage	When plotting, add a line showing the actual coverage?
target_power	When creating boilerplate text for a grant, specify power goal.
mean_gene_length	When making text, specify the mean gene length expected.
nt_per_read	Specify how many reads are in each read(pair).
describe_samples	Add a guestimate of the number of samples required for the power goal.

Value

List containin the various tables and plots returned by PROPER.

See Also

[PROPER] DOI:10.1093/bioinformatics/btu640

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