makeDESeqDF: Converts DESeq results into a data frame to be published

In ReportingTools: Tools for making reports in various formats

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)

ReportingTools documentation built on March 10, 2021, 2 a.m.