IHW (version 1.0.2)

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

Description

ihw.DESeqResults: IHW method dispatching on DESeqResults objects

Usage

"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)