createIndex: Creating an HTML index file

In ArrayTools: geneChip Analysis Package

Description

This HTML index file will link all the ouputted result, including Quality Assessment Report, differentially expressed genes, etc...

Usage

createIndex(..., mydir = getwd(), index.file = "index.html", createHeader = NULL)

Arguments

...	regressionResults or interactionResult
mydir	the directory to contain the index file
index.file	name of the index file
createHeader	If want to want to create an Header, such as your name, company names, etc...

Value

creating an HTML index-file in your directory

Author(s)

Xiwei Wu, Arthur Li

Examples

data(eSetExample)
design<- new("designMatrix", target=pData(eSetExample), covariates = "Treatment")
contrast<- new("contrastMatrix", design.matrix = design, 
    compare1 = "Treated", compare2 = "Control")
result<- regress(eSetExample, contrast)
sigResult<- selectSigGene(result, fc.value=log2(2)) 
## Not run: Output2HTML(sigResult)

design.int<- new("designMatrix", target=pData(eSetExample), covariates = c("Treatment", "Group"),
    intIndex = c(1, 2))
contrast.int<- new("contrastMatrix", design.matrix = design.int, interaction=TRUE)
result.int<- regress(eSetExample, contrast.int)
sigResult.int <- selectSigGene(result.int)
intResult <- postInteraction(eSetExample, sigResult.int, mainVar ="Treatment",
   compare1 = "Treated", compare2 = "Control")
sigResultInt <- selectSigGeneInt(intResult)
## Not run: Output2HTML(sigResultInt)

## Not run: createIndex(sigResult, sigResultInt, createHeader = c("Arthur Li", "COH"))

ArrayTools documentation built on Nov. 8, 2020, 8:13 p.m.