leapp: latent effect adjustment after primary projection

These functions take a gene expression value matrix, a primary covariate vector, an additional known covariates matrix. A two stage analysis is applied to counter the effects of latent variables on the rankings of hypotheses. The estimation and adjustment of latent effects are proposed by Sun, Zhang and Owen (2011). "leapp" is developed in the context of microarray experiments, but may be used as a general tool for high throughput data sets where dependence may be involved.

Author
Yunting Sun <yunting.sun@gmail.com> , Nancy R.Zhang <nzhang@stanford.edu>, Art B.Owen <owen@stanford.edu>
Date of publication
2014-07-22 08:52:54
Maintainer
Yunting Sun <yunting.sun@gmail.com>
License
GPL (>= 2)
Version
1.2

View on CRAN

Man pages

AlternateSVD
Alternating singular value decomposition
FindAUC
Compute the area under the ROC curve (AUC)
FindFpr
Compute the false positive rate at given sizes of retrieved...
FindPrec
compute the precision at given sizes of retrieved genes
FindRec
compute the recall at given sizes of retrieved genes
FindTpr
compute the true positive rate at given sizes of retrieved...
IPOD
Iterative penalized outlier detection algorithm
IPODFUN
compute the iterative penalized outlier detection given the...
leapp
latent effect adjustment after primary projection
leapp-package
latent effect adjustment after primary projection
Pvalue
Calculate statistics and p-values
ridge
Outlier detection with a ridge penalty
ROCplot
plot ROC curve
simdat
Simulated gene expression data affected by a group variable...

Files in this package

leapp
leapp/NAMESPACE
leapp/data
leapp/data/simdat.rda
leapp/R
leapp/R/leapp.R
leapp/MD5
leapp/DESCRIPTION
leapp/man
leapp/man/ROCplot.Rd
leapp/man/FindRec.Rd
leapp/man/FindPrec.Rd
leapp/man/leapp.Rd
leapp/man/ridge.Rd
leapp/man/IPOD.Rd
leapp/man/IPODFUN.Rd
leapp/man/FindTpr.Rd
leapp/man/Pvalue.Rd
leapp/man/leapp-package.Rd
leapp/man/simdat.Rd
leapp/man/FindFpr.Rd
leapp/man/AlternateSVD.Rd
leapp/man/FindAUC.Rd