xps (version 1.32.0)

xpsQAReport: Create Quality Assessment Report.

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.

Value

None, the output is a pdf-file.

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.

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)