ReportingTools (version 2.12.2)

makeDESeqDF: 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

Value

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

Details

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

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)