makeDESeqDF {ReportingTools} | R Documentation

## Converts DESeq results into a data frame to be published

### Description

Manipulates DESeq output to a data frame of significant observations. Draws corresponding box and whisker plots.

### Usage

        makeDESeqDF(object, countTable, pvalueCutoff, conditions,
    annotation.db, expName, reportDir, ...)

### Arguments

`object` | Output from nbinomTest; see DESeq manual for details
`countTable` | A table of the raw counts, where rows indicate genes and columns are samples
`pvalueCutoff` | A threshold value for what is considered a significantly different gene. Only genes with p-values less than this will be included.
`conditions` | A vector indicating the groupings of the samples, for image purposes.
`annotation.db` | A character string, indicating the species of the samples
`expName` | The name of the experiment
`reportDir` | Directory to which the report (and figures) will be written
`...` | Unused arguments passed in from the publish method

### Details

This function converts DESeq output into a data frame and draws the corresponding images

### Value

ret, A data frame with the following values: Entrez Id, Symbol, Gene Name, Image, Log2 Fold Change, P-value and Adjusted p-value.

### Author(s)

Jessica Larson

### Examples

    	#library(DESeq)
    	#library(lattice)
    	#data(mockRnaSeqData)
    	#conditions <- c(rep("case",3), rep("control", 3))
    	#cds<-newCountDataSet(mockRnaSeqData, conditions)
    	#cds<-estimateSizeFactors(cds)
    	#cds<-estimateDispersions(cds)
    	#res<-nbinomTest(cds,"control", "case" )

    	#desReport <- HTMLReport(shortName = 'RNAseq_analysis_with_DESeq',
        #title = 'RNA-seq analysis of differential expression using DESeq',
        #reportDirectory = "./reports")
    	#publish(res,desReport,name="df",countTable=mockRnaSeqData,
        #pvalueCutoff=0.05,
        ##conditions=conditions,annotation.db="org.Mm.eg.db",
        #expName="deseq",reportDir="./reports", .modifyDF=makeDESeqDF)

    #finish(desReport)

[Package ReportingTools version 2.24.0 Index]