Package: phenoTest 1.61.0

Evarist Planet

phenoTest: Tools to test association between gene expression and phenotype in a way that is efficient, structured, fast and scalable. We also provide tools to do GSEA (Gene set enrichment analysis) and copy number variation.

Tools to test correlation between gene expression and phenotype in a way that is efficient, structured, fast and scalable. GSEA is also provided.

Authors:Evarist Planet

phenoTest_1.61.0.tar.gz
phenoTest_1.61.0.zip(r-4.7)phenoTest_1.61.0.zip(r-4.6)phenoTest_1.61.0.zip(r-4.5)
phenoTest_1.61.0.tgz(r-4.6-any)phenoTest_1.61.0.tgz(r-4.5-any)
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phenoTest_1.61.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION
card.svg |card.png
phenoTest/json (API)

# Install 'phenoTest' in R:

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

Datasets:

epheno - Epheno object.
eset - Example data.
eset.genelevel - Example data.

On BioConductor:phenoTest-1.61.0(bioc 3.24)phenoTest-1.60.0(bioc 3.23)

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

microarray differentialexpression multiplecomparison clustering classification

4.97 score 1 packages 26 scripts 6 mentions 44 exports 130 dependencies

Last updated from:9c9fc2085a. Checks:1 ERROR, 7 NOTE, 2 OK. Indexed: yes.

Target	Result	Time
bioc-checks	ERROR	341
linux-devel-x86_64	NOTE	499
source / vignettes	OK	329
linux-release-x86_64	NOTE	443
macos-release-arm64	NOTE	276
macos-oldrel-arm64	NOTE	266
windows-devel	NOTE	331
windows-release	NOTE	304
windows-oldrel	NOTE	328
wasm-release	OK	229

Exports:approach barplotSignatures barplotSignifSignatures ClusterPhenoTest epheno2html eset2genelevel export2CSV ExpressionPhenoTest findCopyNumber genesInArea getEs getEsPositions getEsSim getFc getFcHr getHr getMeans getPostProbs getPvals getSignif getSummaryDif getVars2test gsea gsea.selGsets gsea.selVars gsea2html gseaSignatures gseaSignificance heatmapPhenoTest logFcHr p.adjust.method pAdjust pca phenoClass phenoNames plot.gseaData plot.gseaSignaturesSign plot.gseaSignaturesVar show smoothCoxph summary.gseaData summary.gseaSignificanceSign summary.gseaSignificanceVar write.html

Dependencies:annotate AnnotationDbi askpass backports base64enc BH Biobase BiocFileCache BiocGenerics biomaRt Biostrings bit bit64 bitops blob BMA bslib cachem Category caTools checkmate cli cluster colorspace cpp11 crayon curl data.table DBI dbplyr DEoptimR digest dplyr ellipse evaluate farver fastmap filelock fontawesome foreign Formula fs genefilter generics ggplot2 glue gplots graph gridExtra GSEABase gtable gtools Heatplus hgu133a.db highr Hmisc hms hopach htmlTable htmltools htmlwidgets httr httr2 inline IRanges isoband jquerylib jsonlite KEGGREST KernSmooth knitr labeling lattice leaps lifecycle limma magrittr Matrix MatrixGenerics matrixStats memoise mgcv mime mvtnorm nlme nnet openssl org.Hs.eg.db pcaPP pillar pkgconfig png prettyunits progress purrr R6 rappdirs RBGL RColorBrewer rlang rmarkdown robustbase rpart rrcov RSQLite rstudioapi S4Vectors S7 sass scales Seqinfo statmod stringi stringr survival sys tibble tidyr tidyselect tinytex utf8 vctrs viridisLite withr xfun XML xml2 xtable XVector yaml

Manual for the phenoTest library

Introduction | Individual gene(s) association with phenotype(s) | Gene set(s) association with phenotype(s)

Rendered fromphenoTest.Rnwusingutils::Sweave

Last update: 2019-12-17
Started: 2013-11-01

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
Test correlation between gene expression and phenotype.	phenoTest-package phenoTest
Summary plots for gene signature vs phenotype association	barplotSignatures barplotSignifSignatures
Methods for Function barplotSignatures in Package `phenoTest'	barplotSignatures,epheno,character-method barplotSignatures,epheno,GeneSet-method barplotSignatures,epheno,GeneSetCollection-method barplotSignatures,epheno,list-method barplotSignatures-methods
Methods for Function barplotSignifSignatures in Package `phenoTest'	barplotSignifSignatures,epheno,character-method barplotSignifSignatures,epheno,GeneSet-method barplotSignifSignatures,epheno,GeneSetCollection-method barplotSignifSignatures,epheno,list-method barplotSignifSignatures-methods
Test association of clusters with phenotype.	ClusterPhenoTest
epheno object.	epheno
Class "epheno"	approach,epheno-method dim,epheno-method epheno-class getFc,epheno-method getHr,epheno-method getMeans,epheno-method getPostProbs,epheno-method getPvals,epheno-method getSignif,epheno-method getSummaryDif,epheno-method logFcHr,epheno-method p.adjust.method,epheno-method phenoClass,epheno-method phenoNames,epheno-method show,epheno-method [,epheno,ANY,ANY-method
Create html files and plots from an epheno object.	epheno2html
Example data.	eset
Example data.	eset.genelevel
Filter ExpressionSet to keep one probeset per gene.	eset2genelevel
Export object to comma-separated text file.	export2CSV
Methods for Function export2CSV in Package 'phenoTest'	export2CSV,epheno-method export2CSV-methods
Tests univariate association between a list of phenotype variables and gene expression.	ExpressionPhenoTest
Find copy number regions using expression data in a similar way ACE does.	findCopyNumber
Find genes that are in given areas.	genesInArea
Substract element's of a gseaSignaturesSign or gseaSignaturesVar object (obtained using the gseaSignatures function).	getEs getEsSim getFcHr getNes
Obtain chromosome positions for each gene.	getEsPositions
Getters for the epheno object:	approach getFc getHr getMeans getPostProbs getPvals getSignif getSummaryDif logFcHr p.adjust.method phenoClass phenoNames [,epheno,ANY,ANY,ANY-method
Get phenotypic variables that were tested.	getVars2test
Methods for Function getVars2test in Package `phenoTest'	getVars2test,epheno-method getVars2test-methods
GSEA (Gene Set Enrichment Analysis).	gsea
Subset an object of class gseaData.	gsea.selGsets gsea.selVars
Export an object of class gseaData to an html file.	gsea2html
Class "gseaData"	getEs,gseaData-method getEsSim,gseaData-method getFcHr,gseaData-method gseaData-class show,gseaData-method
Compute ES (enrichment scores) and es.sim (simulated enrichment scores) for given phenotipic variable(s) and signature(s).	gseaSignatures
Class "gseaSignatures" ES and EsSim container.	gseaSignatures-class
Methods for Function gseaSignatures in Package `phenoTest'	gseaSignatures,ANY,character-method gseaSignatures,ANY,GeneSet-method gseaSignatures,epheno,GeneSetCollection-method gseaSignatures,epheno,list-method gseaSignatures,matrix,GeneSetCollection-method gseaSignatures,matrix,list-method gseaSignatures,numeric,GeneSetCollection-method gseaSignatures,numeric,list-method gseaSignatures-methods
Class "gseaSignaturesSign"	getEs,gseaSignaturesSign-method getEsSim,gseaSignaturesSign-method getFcHr,gseaSignaturesSign-method gseaSignaturesSign-class gseaSignificance,gseaSignaturesSign-method
Class "gseaSignaturesVar"	getEs,gseaSignaturesVar-method getEsSim,gseaSignaturesVar-method getFcHr,gseaSignaturesVar-method gseaSignaturesVar-class gseaSignificance,gseaSignaturesVar-method
ES' (enrichment scores) sifgnificance.	gseaSignificance
Class "gseaSignificanceSign"	gseaSignificanceSign-class
Class "gseaSignificanceVar"	gseaSignificanceVar-class
Produce heatmap from phenotype data.	heatmapPhenoTest
Methods for Function heatmapPhenoTest in Package `phenoTest'	heatmapPhenoTest,ExpressionSet,character-method heatmapPhenoTest,ExpressionSet,GeneSet-method heatmapPhenoTest,ExpressionSet,GeneSetCollection-method heatmapPhenoTest,ExpressionSet,list-method heatmapPhenoTest,ExpressionSet,missing-method heatmapPhenoTest-methods
Adjust p values of an epheno object.	pAdjust
Methods for Function pAdjust in Package `phenoTest'	pAdjust,epheno-method pAdjust-methods
Principal components plot.	pca
GSEA-like Plot.	plot.gseaData
GSEA-like Plot.	plot.gseaSignaturesSign plot.gseaSignaturesVar
Methods for Function show in Package `methods'.	show,AnnotatedDataFrame-method show,ANY-method show,classRepresentation-method show,container-method show,eSet-method show,genericFunction-method show,gseaSignaturesSign-method show,gseaSignaturesVar-method show,gseaSignificanceSign-method show,gseaSignificanceVar-method show,LargeDataObject-method show,MethodDefinition-method show,MethodSelectionReport-method show,MethodWithNext-method show,MIAME-method show,namedList-method show,ObjectsWithPackage-method show,oldClass-method show,ScalarCharacter-method show,ScalarObject-method show,signature-method show,TestResults-method show,traceable-method show,Versioned-method show,Versions-method show,VersionsNull-method show-methods
Plots the Cox proportional hazard smoothed by gene expression level.	smoothCoxph
Obtain a data.frame with the pvalues and fdr for all signatures and variables of a gseaData object.	summary.gseaData
Obtain a data.frame with the pvalues and fdr for all signatures and variables of a gseaSignificanceSign or gseaSignificanceVar object.	summary.gseaSignificanceSign summary.gseaSignificanceVar
Write a data.frame to an html file.	write.html