Package: leapp 1.3

Yunting Sun

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.

Authors:Yunting Sun <[email protected]> , Nancy R.Zhang <[email protected]>, Art B.Owen <[email protected]>

leapp_1.3.tar.gz
leapp_1.3.tar.gz(r-4.5-noble)leapp_1.3.tar.gz(r-4.4-noble)
leapp_1.3.tgz(r-4.4-emscripten)leapp_1.3.tgz(r-4.3-emscripten)
leapp.pdf |leapp.html✨
leapp/json (API)

# Install 'leapp' in R:

install.packages('leapp', repos = c('https://cran.r-universe.dev', 'https://cloud.r-project.org'))

Datasets:

simdat - Simulated gene expression data affected by a group variable and an unobserved factor

This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.

11 exports 0.00 score 64 dependencies 9 scripts 204 downloads

Last updated 2 years agofrom:bce08cc7d0. Checks:OK: 1 NOTE: 1. Indexed: yes.

Target	Result	Date
Doc / Vignettes	OK	Sep 05 2024
R-4.5-linux	NOTE	Sep 05 2024

Exports:AlternateSVD FindAUC FindFpr FindPrec FindRec FindTpr IPOD IPODFUN leapp ridge ROCplot

Dependencies:annotate AnnotationDbi askpass BH Biobase BiocGenerics BiocParallel Biostrings bit bit64 blob cachem cli codetools corpcor cpp11 crayon curl DBI edgeR fastmap formatR futile.logger futile.options genefilter GenomeInfoDb GenomeInfoDbData glue httr IRanges jsonlite KEGGREST lambda.r lattice lifecycle limma locfit MASS Matrix MatrixGenerics matrixStats memoise mgcv mime nlme openssl pkgconfig plogr png R6 rlang RSQLite S4Vectors snow statmod survival sva sys UCSC.utils vctrs XML xtable XVector zlibbioc

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

Package: leapp 1.3

leapp: Latent Effect Adjustment After Primary Projection

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