iCheck: QC Pipeline and Data Analysis Tools for High-Dimensional Illumina mRNA Expression Data
Version 1.6.0

QC pipeline and data analysis tools for high-dimensional Illumina mRNA expression data.

AuthorWeiliang Qiu [aut, cre], Brandon Guo [aut, ctb], Christopher Anderson [aut, ctb], Barbara Klanderman [aut, ctb], Vincent Carey [aut, ctb], Benjamin Raby [aut, ctb]
Bioconductor views DNAMethylation DifferentialExpression GeneExpression Microarray OneChannel Preprocessing QualityControl TwoChannel
Date of publicationNone
MaintainerWeiliang Qiu <stwxq@channing.harvard.edu>
LicenseGPL (>= 2)
Version1.6.0
Package repositoryView on Bioconductor
InstallationInstall the latest version of this package by entering the following in R:
source("https://bioconductor.org/biocLite.R")
biocLite("iCheck")

Popular man pages

boxPlots: Draw parallel plots for top results in whole-genome-wide...
densityPlots: Draw estimated density plots for all arrays
genExprSet: Generate an ExpressionSet object
lmFitPaired: A wrapper function for the function 'lmFit' of the R...
lmFitWrapper: A wrapper function for the function 'lmFit' of the R...
LumiBatch2Table: Output slots (exprs, pData, fData) of an LumiBatch object...
quantilePlot: Plot trajectories of quantiles across arrays
See all...

All man pages Function index File listing

Man pages

boxPlots: Draw parallel plots for top results in whole-genome-wide...
densityPlots: Draw estimated density plots for all arrays
genExprSet: Generate an ExpressionSet object
genSimData.BayesNormal: Generating simulated data set from conditional normal...
getPCAFunc: Get principal components of arrays
glmWrapper: Perform glm test for all gene probes
lkhrWrapper: Perform glm test for all gene probes
lmFitPaired: A wrapper function for the function 'lmFit' of the R...
lmFitWrapper: A wrapper function for the function 'lmFit' of the R...
LumiBatch2Table: Output slots (exprs, pData, fData) of an LumiBatch object...
pca2DPlot: Scatter plot of first 2 principal components
pca3DPlot: Scatter plot of 3 specified principal components
plotCurves: Plot trajectories of probe profiles across arrays
plotQCCurves: Plot trajectories of specific QC probes (e.g., biotin,...
plotSamplep95p05: Plot trajectories of the ratio of 95th percentile to 5th...
quantilePlot: Plot trajectories of quantiles across arrays
R2PlotFunc: Draw heatmap of square of correlations among arrays
scatterPlots: Draw scatter plots for top results in whole-genome-wide...
sortExpressionSet: Sort the order of samples for an ExpressionSet object

Functions

LumiBatch2Table Man page Source code
R2PlotFunc Man page Source code
addfDat Source code
boxPlots Man page Source code
checkCovariate Source code
densityPlots Man page Source code
extractIDs Source code
extractIDs3 Source code
extractSamples Source code
genExprSet Man page Source code
genSimData.BayesNormal Man page Source code
getCovInterest Source code
getDatColnames Source code
getDesignMat.glm Source code
getPCAFunc Man page Source code
glmFitOneProbe Source code
glmWrapper Man page Source code
inputChecking Source code
lkhrFitOneProbe Source code
lkhrWrapper Man page Source code
lmFitPaired Man page Source code
lmFitWrapper Man page Source code
logit Source code
mergeDuplicates Source code
myCombine Source code
myCombineIntersect Source code
myCombineUnion Source code
myShow Source code
outputFunc Source code
outputFunc2 Source code
pca2DPlot Man page Source code
pca3DPlot Man page Source code
plotCurves Man page Source code
plotQCCurves Man page Source code
plotSamplep95p05 Man page Source code
quantilePlot Man page Source code
readData Source code
readData.default Source code
readbgx Source code
readbgx2 Source code
scatterPlots Man page Source code
separateGCnonGC Source code
sortExpressionSet Man page Source code
upperTriangle Source code

Files

DESCRIPTION
INDEX
NAMESPACE
NEWS
R
R/LumiBatch2Table.R
R/genExprSet.R
R/genSimData.BayesNormal.R
R/glmWrapper.R
R/lmFitPaired.R
R/lmFitWrapper.R
R/myCombine.R
R/myShow.R
R/plotFuncs.R
R/readData.R
R/readbgx.R
build
build/vignette.rds
inst
inst/doc
inst/doc/iCheck.R
inst/doc/iCheck.Rnw
inst/doc/iCheck.pdf
man
man/LumiBatch2Table.Rd
man/R2PlotFunc.Rd
man/boxPlots.Rd
man/densityPlots.Rd
man/genExprSet.Rd
man/genSimData.BayesNormal.Rd
man/getPCAFunc.Rd
man/glmWrapper.Rd
man/lkhrWrapper.Rd
man/lmFitPaired.Rd
man/lmFitWrapper.Rd
man/pca2DPlot.Rd
man/pca3DPlot.Rd
man/plotCurves.Rd
man/plotQCCurves.Rd
man/plotSamplep95p05.Rd
man/quantilePlot.Rd
man/scatterPlots.Rd
man/sortExpressionSet.Rd
vignettes
vignettes/iCheck.Rnw
iCheck documentation built on May 20, 2017, 10:03 p.m.

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