leapp: latent effect adjustment after primary projection
Version 1.2

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.

Browse man pages Browse package API and functions Browse package files

AuthorYunting Sun <yunting.sun@gmail.com> , Nancy R.Zhang <nzhang@stanford.edu>, Art B.Owen <owen@stanford.edu>
Date of publication2014-07-22 08:52:54
MaintainerYunting Sun <yunting.sun@gmail.com>
LicenseGPL (>= 2)
Version1.2
Package repositoryView on CRAN
InstallationInstall the latest version of this package by entering the following in R:
install.packages("leapp")

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...

Functions

AlternateSVD Man page Source code
FindAUC Man page Source code
FindFpr Man page Source code
FindPrec Man page Source code
FindRec Man page Source code
FindTpr Man page Source code
IPOD Man page Source code
IPODFUN Man page Source code
Pvalue Man page Source code
ROCplot Man page Source code
leapp Man page Source code
leapp-package Man page
ridge Man page Source code
simdat Man page

Files

NAMESPACE
data
data/simdat.rda
R
R/leapp.R
MD5
DESCRIPTION
man
man/ROCplot.Rd
man/FindRec.Rd
man/FindPrec.Rd
man/leapp.Rd
man/ridge.Rd
man/IPOD.Rd
man/IPODFUN.Rd
man/FindTpr.Rd
man/Pvalue.Rd
man/leapp-package.Rd
man/simdat.Rd
man/FindFpr.Rd
man/AlternateSVD.Rd
man/FindAUC.Rd
leapp documentation built on May 20, 2017, 3:09 a.m.