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

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

Author
Weiliang Qiu [aut, cre], Brandon Guo [aut, ctb], Christopher Anderson [aut, ctb], Barbara Klanderman [aut, ctb], Vincent Carey [aut, ctb], Benjamin Raby [aut, ctb]
Date of publication
None
Maintainer
Weiliang Qiu <stwxq@channing.harvard.edu>
License
GPL (>= 2)
Version
1.4.0

View on Bioconductor

Man pages

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
sortExpressionSet
Sort the order of samples for an ExpressionSet object

Files in this package

iCheck/DESCRIPTION
iCheck/INDEX
iCheck/NAMESPACE
iCheck/NEWS
iCheck/R
iCheck/R/LumiBatch2Table.R
iCheck/R/genExprSet.R
iCheck/R/genSimData.BayesNormal.R
iCheck/R/glmWrapper.R
iCheck/R/lmFitPaired.R
iCheck/R/lmFitWrapper.R
iCheck/R/myCombine.R
iCheck/R/myShow.R
iCheck/R/plotFuncs.R
iCheck/R/readData.R
iCheck/R/readbgx.R
iCheck/build
iCheck/build/vignette.rds
iCheck/inst
iCheck/inst/doc
iCheck/inst/doc/iCheck.R
iCheck/inst/doc/iCheck.Rnw
iCheck/inst/doc/iCheck.pdf
iCheck/man
iCheck/man/LumiBatch2Table.Rd
iCheck/man/R2PlotFunc.Rd
iCheck/man/genExprSet.Rd
iCheck/man/genSimData.BayesNormal.Rd
iCheck/man/getPCAFunc.Rd
iCheck/man/glmWrapper.Rd
iCheck/man/lkhrWrapper.Rd
iCheck/man/lmFitPaired.Rd
iCheck/man/lmFitWrapper.Rd
iCheck/man/pca2DPlot.Rd
iCheck/man/pca3DPlot.Rd
iCheck/man/plotCurves.Rd
iCheck/man/plotQCCurves.Rd
iCheck/man/plotSamplep95p05.Rd
iCheck/man/quantilePlot.Rd
iCheck/man/sortExpressionSet.Rd
iCheck/vignettes
iCheck/vignettes/iCheck.Rnw