ihw_adjust: Make sure the outputs from limma and friends are in a format...

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

Make sure the outputs from limma and friends are in a format suitable for IHW.

Description

IHW seems like an excellent way to improve the confidence in the p-values provided by the various DE methods. It expects inputs fairly specific to DESeq2, however, it is trivial to convert other methods to this, ergo this function.

Usage

ihw_adjust(
  de_result,
  pvalue_column = "pvalue",
  type = NULL,
  mean_column = "baseMean",
  significance = 0.05
)

Arguments

de_result	Table which should have the 2 types of requisite columns: mean value of counts and p-value.
pvalue_column	Name of the column of p-values.
type	If specified, this will explicitly perform the calculation for the given type of differential expression analysis: limma, edger, deseq, etc.
mean_column	Name of the column of mean values.
significance	IHW uses this parameter, I don't know why.

Details

https://bioconductor.org/packages/release/bioc/vignettes/IHW/inst/doc/introduction_to_ihw.html

Value

weight adjusted p-values.

See Also

[IHW]

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