Description Usage Arguments Details Value Note Author(s) Examples
Create a quality assessment report.
1 2 3 4 5 6 7 8 9 10 11 12 13 |
xps.data |
object of class |
xps.expr |
object of class |
xps.call |
object of class |
xps.qual |
object of class |
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 |
overwrite |
logical, if |
verbose |
logical, if |
... |
optional arguments to be passed to |
Function xpsQAReport
creates a quality assessment report "QAReport.pdf" for all TreeSet
s,
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
.
None, the output is a pdf-file.
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.
Christian Stratowa, based on ideas of package affyQCReport.
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 | ## 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)
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