ihw.DESeqResults: ihw.DESeqResults: IHW method dispatching on DESeqResults...

In nignatiadis/IHW: Independent Hypothesis Weighting

ihw.DESeqResults: IHW method dispatching on DESeqResults objects

Description

ihw.DESeqResults: IHW method dispatching on DESeqResults objects

Usage

## S3 method for class 'DESeqResults'
ihw(deseq_res, filter = "baseMean", alpha = 0.1, adjustment_type = "BH", ...)

Arguments

deseq_res	"DESeqResults" object
filter	Vector of length equal to number of rows of deseq_res object. This is used for the covariates in the call to ihw. Can also be a character, in which case deseq_res[[filter]] is used as the covariate
alpha	Numeric, sets the nominal level for FDR control.
adjustment_type	Character ("BH" or "bonferroni") depending on whether you want to control FDR or FWER.
...	Other optional keyword arguments passed to ihw.

Value

A "DESeqResults" object, which includes weights and adjusted p-values returned by IHW. In addition, includes a metadata slot with an "ihwResult" object.

See Also

ihw, ihwResult

Examples

## Not run: 
   library("DESeq2")
   library("airway")
   data("airway")
   dds <- DESeqDataSet(se = airway, design = ~ cell + dex)
   dds <- DESeq(dds)
   deseq_res <- results(dds)
   deseq_res <- ihw(deseq_res, alpha=0.1)
   #equivalent: deseq_res2 <- results(dds, filterFun = ihw)

## End(Not run)

nignatiadis/IHW documentation built on Aug. 22, 2023, 2:11 p.m.