xpsQAReport: Create Quality Assessment Report.

In xps: Processing and Analysis of Affymetrix Oligonucleotide Arrays including Exon Arrays, Whole Genome Arrays and Plate Arrays

Description

Create a quality assessment report.

Usage

xpsQAReport(xps.data,
            xps.expr    = NULL,
            xps.call    = NULL,
            xps.qual    = NULL,
            dataset     = character(0), 
            title       = "Quality Report",
            date        = "October, 2011",
            author      = "Christian Stratowa",
            outdir      = file.path(getwd(), "QAReport"),
            add.pseudo  = FALSE,
            overwrite   = FALSE,
            verbose     = TRUE,
            ...) 

Arguments

xps.data	object of class DataTreeSet.
xps.expr	object of class ExprTreeSet.
xps.call	object of class CallTreeSet.
xps.qual	object of class QualTreeSet.
dataset	name of the dataset.
title	title of quality report.
date	date of quality report.
author	author(s) of quality report.
outdir	name of directory where to create the quality report.
add.pseudo	logical, if TRUE add pseudo-images to the quality report.
overwrite	logical, if TRUE overwrite outdir and its contents.
verbose	logical, if TRUE print status information.
...	optional arguments to be passed to xpsQAReport.

Details

Function xpsQAReport creates a quality assessment report "QAReport.pdf" for all TreeSets, which are passed as parameters to the function. It calls library(tools) and uses its function buildVignettes to create the report.

If parameter xps.qual is supplied, it is possible to create pseudo-images for every CEL-file by setting parameter add.pseudo=TRUE.

Value

None, the output is a pdf-file.

Note

Function xpsQAReport requires a working LaTeX implementation and so will only work on Windows platforms, and on OS X, if the user has installed the necessary LaTeX tools.

Author(s)

Christian Stratowa, based on ideas of package affyQCReport.

Examples

## Not run: 
 ## first, load ROOT scheme file and ROOT data file
 scheme.test3 <- root.scheme(paste(path.package("xps"),"schemes/SchemeTest3.root",sep="/"))
 data.test3 <- root.data(scheme.test3, paste(path.package("xps"),"rootdata/DataTest3_cel.root",sep="/"))

 ## optional normalized expression levels
 data.rma <- rma(data.test3,"Test3RMA",tmpdir="",background="pmonly",normalize=TRUE,verbose=FALSE)

 ## optional MAS5 detection call
 call.mas5 <- mas5.call(data.test3,"Test3Call",tmpdir="",verbose=FALSE)

 ## optional quality measures
 rlm.all <- rmaPLM(data.test3, "tmp_Test3RLMall", filedir=getwd(), tmpdir="", qualopt="all", option="transcript", add.data=FALSE)

 ## quality assessment report
 xpsQAReport(data.test3, data.rma, call.mas5, rlm.all, dataset="My Dataset", add.pseudo=TRUE, overwrite=TRUE)

## End(Not run)

xps documentation built on Nov. 8, 2020, 6 p.m.