hpgl_voomweighted: A minor change to limma's voom with quality weights to...

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

A minor change to limma's voom with quality weights to attempt to address some corner cases.

Description

This copies the logic employed in hpgl_voom(). I suspect one should not use it.

Usage

hpgl_voomweighted(
  data,
  fun_model,
  libsize = NULL,
  normalize.method = "none",
  plot = TRUE,
  span = 0.5,
  var.design = NULL,
  method = "genebygene",
  maxiter = 50,
  tol = 1e-10,
  trace = FALSE,
  replace.weights = TRUE,
  col = NULL,
  ...
)

Arguments

data	Some data!
fun_model	A model for voom() and arrayWeights()
libsize	Library sizes passed to voom().
normalize.method	Passed to voom()
plot	Do the plot of mean variance?
span	yes
var.design	maybe
method	kitty!
maxiter	50 is good
tol	I have no tolerance.
trace	no trace for you.
replace.weights	Replace the weights?
col	yay columns!
...	more arguments!

Value

a voom return

See Also

[limma::voom()]

Examples

## Not run: 
## No seriously, dont run this, I think it is wiser to use the functions
## provided by limma. But this provides a place to test stuff out.
 voom_result <- hpgl_voomweighted(dataset, model)

## End(Not run)

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