runIHW: Apply Independent Hypothesis Weighting (IHW) to a list of...

In DGEobj.utils: Differential Gene Expression (DGE) Analysis Utility Toolkit

Apply Independent Hypothesis Weighting (IHW) to a list of topTable dataframes

Description

This is a wrapper around the independent hypothesis weighting package that takes a list of topTable data frames and applies Independent Hypothesis Weighting (IHW) to each topTable data frame in the list.

Usage

runIHW(contrastList, alpha = 0.1, FDRthreshold = 0.1, ...)

Arguments

contrastList	A named list of topTable dataframes.
alpha	Alpha should be the desired FDR level to interrogate (range 0-1; Default = 0.1)
FDRthreshold	Threshold value for the p-values of a dataframe (Default = 0.1)
...	other arguments are passed directly to the ihw function (see ?ihw)

Details

IHW is a method developed by N. Ignatiadis (http://dx.doi.org/10.1101/034330) to weight FDR values based on a covariate (AveExpr in this case).

The IHW FDR values are added as additional columns to the topTable data frames.

Function runIHW is normally called by runContrasts with argument IHW=T. It can also be used independently on a list of topTable dataframes. A list of topTable dataframes is conveniently retrieved with the DGEobj::getType function with the type argument set to "topTable".

This function expects the following columns are present in each data frame: P.value, adj.P.Val, AveExpr.

Note that it is impractical to run IHW on a list of genes less than ~5000. Operationally, IHW breaks the data into bins of 1500 genes for the analysis. If bins = 1, IHW converges on the BH FDR value. Instead, run IHW on the complete set of detected genes from topTable (not topTreat) results.

Value

A list of lists. The first element is the original contrastList with additional IHW columns added to each dataframe. The topTable dataframes will contain additional columns added by the IHW analysis and prefixed with "ihw." The second list element is the IHW result dataframe.

Examples

## Not run: 
   # NOTE: Requires the IHW package

   dgeObj <- readRDS(system.file("exampleObj.RDS", package = "DGEobj"))
   contrastList <- DGEobj::getType(dgeObj, type = "topTable")
   contrastList <- lapply(contrastList, dplyr::select,
                          -ihw.adj_pvalue,
                          -ihw.weight,
                          -ihw.weighted_pvalue)
   colnames(contrastList[[1]])
   contrastList <- runIHW(contrastList)

   # note new columns added
   colnames(contrastList[["contrasts"]][[1]])

## End(Not run)

DGEobj.utils documentation built on May 20, 2022, 1:08 a.m.