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

Description Usage Arguments Value See Also Examples

View source: R/ihw_convex.R

Description

ihw.DESeqResults: IHW method dispatching on DESeqResults objects

Usage

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## 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

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## 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)

IHW documentation built on Nov. 8, 2020, 7:44 p.m.