Package: genefu 2.45.0

Benjamin Haibe-Kains

genefu: Computation of Gene Expression-Based Signatures in Breast Cancer

This package contains functions implementing various tasks usually required by gene expression analysis, especially in breast cancer studies: gene mapping between different microarray platforms, identification of molecular subtypes, implementation of published gene signatures, gene selection, and survival analysis.

Authors:Deena M.A. Gendoo [aut], Natchar Ratanasirigulchai [aut], Markus S. Schroeder [aut], Laia Pare [aut], Joel S Parker [aut], Aleix Prat [aut], Nikta Feizi [ctb], Christopher Eeles [ctb], Jermiah Joseph [ctb], Benjamin Haibe-Kains [aut, cre]

genefu_2.45.0.tar.gz
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genefu_2.45.0.tgz(r-4.6-any)genefu_2.45.0.tgz(r-4.5-any)
genefu_2.45.0.tar.gz(r-4.7-any)genefu_2.45.0.tar.gz(r-4.6-any)
genefu_2.45.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
genefu/json (API)

# Install 'genefu' in R:

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

Datasets:

annot.expos - Gene expression, annotations and clinical data from the International Genomics Consortium
annot.nkis - Gene expression, annotations and clinical data from van de Vijver et al. 2002
annot.vdxs - Gene expression, annotations and clinical data from Wang et al. 2005 and Minn et al 2007
claudinLowData - ClaudinLowData for use in the claudinLow classifier. Data generously provided by Aleix Prat.
data.expos - Gene expression, annotations and clinical data from the International Genomics Consortium
data.nkis - Gene expression, annotations and clinical data from van de Vijver et al. 2002
data.vdxs - Gene expression, annotations and clinical data from Wang et al. 2005 and Minn et al 2007
demo.expos - Gene expression, annotations and clinical data from the International Genomics Consortium
demo.nkis - Gene expression, annotations and clinical data from van de Vijver et al. 2002
demo.vdxs - Gene expression, annotations and clinical data from Wang et al. 2005 and Minn et al 2007
mod1 - Gene modules published in Desmedt et al. 2008
mod2 - Gene modules published in Wirapati et al. 2008
modelOvcAngiogenic - Model used to classify ovarian tumors into Angiogenic and NonAngiogenic subtypes.
pam50 - PAM50 classifier for identification of breast cancer molecular subtypes
pam50.robust - PAM50 classifier for identification of breast cancer molecular subtypes
pam50.scale - PAM50 classifier for identification of breast cancer molecular subtypes
scmgene.robust - Subtype Clustering Model using only ESR1, ERBB2 and AURKA genes for identification of breast cancer molecular subtypes
scmod1.robust - Subtype Clustering Model using ESR1, ERBB2 and AURKA modules for identification of breast cancer molecular subtypes
scmod2.robust - Subtype Clustering Model using ESR1, ERBB2 and AURKA modules for identification of breast cancer molecular subtypes
sig.endoPredict - Signature used to compute the endoPredict signature as published by Filipits et al 2011
sig.gene70 - Signature used to compute the 70 genes prognosis profile (GENE70) as published by van't Veer et al. 2002
sig.gene76 - Signature used to compute the Relapse Score (GENE76) as published in Wang et al. 2005
sig.genius - Gene Expression progNostic Index Using Subtypes (GENIUS) as published by Haibe-Kains et al. 2010.
sig.ggi - Gene expression Grade Index (GGI) as published in Sotiriou et al. 2006
sig.oncotypedx - Signature used to compute the OncotypeDX signature as published by Paik et al 2004
sig.pik3cags - Gene expression Grade Index (GGI) as published in Sotiriou et al. 2006
sig.tamr13 - Tamoxifen Resistance signature composed of 13 gene clusters (TAMR13) as published by Loi et al. 2008.
sigOvcAngiogenic - SigOvcAngiogenic dataset
sigOvcCrijns - SigOvcCrijns dataset
sigOvcSpentzos - SigOcvSpentzos dataset
sigOvcTCGA - SigOvcTCGA dataset
sigOvcYoshihara - SigOvcYoshihara dataset
ssp2003 - SSP2003 classifier for identification of breast cancer molecular subtypes
ssp2003.robust - SSP2003 classifier for identification of breast cancer molecular subtypes
ssp2003.scale - SSP2003 classifier for identification of breast cancer molecular subtypes
ssp2006 - SSP2006 classifier for identification of breast cancer molecular subtypes
ssp2006.robust - SSP2006 classifier for identification of breast cancer molecular subtypes
ssp2006.scale - SSP2006 classifier for identification of breast cancer molecular subtypes

On BioConductor:genefu-2.45.0(bioc 3.24)genefu-2.44.0(bioc 3.23)

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

differentialexpression geneexpression visualization clustering classification

7.41 score 3 packages 286 scripts 42 mentions 50 exports 107 dependencies

Last updated from:09a9b1dc52. Checks:8 WARNING, 2 OK. Indexed: yes.

Target	Result	Time
bioc-checks	WARNING	210
linux-devel-x86_64	WARNING	275
source / vignettes	OK	294
linux-release-x86_64	WARNING	271
macos-release-arm64	WARNING	172
macos-oldrel-arm64	WARNING	225
windows-devel	WARNING	223
windows-release	WARNING	188
windows-oldrel	WARNING	192
wasm-release	OK	177

Exports:bimod boxplotplus2 claudinLow collapseIDs compareProtoCor compute.pairw.cor.meta compute.pairw.cor.z compute.proto.cor.meta cordiff.dep endoPredict fuzzy.ttest gene70 gene76 geneid.map genius ggi ihc4 intrinsic.cluster intrinsic.cluster.predict map.datasets medianCtr molecular.subtyping npi oncotypedx ovcAngiogenic ovcCrijns ovcTCGA ovcYoshihara overlapSets pik3cags power.cor ps.cluster read.m.file readArray rename.duplicate rescale rorS setcolclass.df sig.score spearmanCI st.gallen stab.fs stab.fs.ranking strescR subtype.cluster subtype.cluster.predict tamr13 tbrm weighted.meanvar write.m.file

Dependencies:AIMS amap AnnotationDbi askpass Biobase BiocFileCache BiocGenerics biomaRt Biostrings bit bit64 blob bootstrap cachem class cli cluster codetools cpp11 crayon curl data.table DBI dbplyr diagram digest dplyr e1071 farver fastmap filelock future future.apply generics ggplot2 globals glue gtable hms httr httr2 iC10 iC10TrainingData impute ipred IRanges isoband jsonlite KEGGREST KernSmooth labeling lattice lava lifecycle limma listenv magrittr MASS Matrix mclust memoise mime nnet numDeriv openssl pamr parallelly pillar pkgconfig png prettyunits prodlim progress progressr proxy purrr R6 rappdirs RColorBrewer Rcpp rlang rmeta rpart RSQLite S4Vectors S7 scales Seqinfo shape SQUAREM statmod stringi stringr SuppDists survcomp survival survivalROC sys tibble tidyr tidyselect utf8 vctrs viridisLite withr xml2 XVector

genefu: A Package for Breast Cancer Gene Expression Analysis

Rendered fromgenefu.Rmdusingknitr::rmarkdown

Last update: 2021-05-21
Started: 2021-01-12

Help page	Topics
Function to identify bimodality for gene expression or signature score	bimod
Box plot of group of values with corresponding jittered points	boxplotplus2
Claudin-low classification for Breast Cancer Data	claudinLow
claudinLowData for use in the claudinLow classifier. Data generously provided by Aleix Prat.	claudinLowData
Utility function to collapse IDs	collapseIDs
Function to statistically compare correlation to prototypes	compareProtoCor
Function to compute pairwise correlations in a meta-analytical framework	compute.pairw.cor.meta
Function to compute the Z transformation of the pairwise correlations for a list of datasets	compute.pairw.cor.z
Function to compute correlations to prototypes in a meta-analytical framework	compute.proto.cor.meta
Function to estimate whether two dependent correlations differ	cordiff.dep
Function to compute the endoPredict signature as published by Filipits et al 2011	endoPredict
Gene expression, annotations and clinical data from the International Genomics Consortium	annot.expos data.expos demo.expos expos
Function to compute the fuzzy Student t test based on weighted mean and weighted variance	fuzzy.ttest
Function to compute the 70 genes prognosis profile (GENE70) as published by van't Veer et al. 2002	gene70
Function to compute the Relapse Score as published by Wang et al. 2005	gene76
Function to find the common genes between two datasets or a dataset and a gene list	geneid.map
Function to compute the Gene Expression progNostic Index Using Subtypes (GENIUS) as published by Haibe-Kains et al. 2010	genius
Function to compute the raw and scaled Gene expression Grade Index (GGI)	ggi
Function to compute the IHC4 prognostic score as published by Paik et al. in 2004.	ihc4
Function to fit a Single Sample Predictor (SSP) as in Perou, Sorlie, Hu, and Parker publications	intrinsic.cluster
Function to identify breast cancer molecular subtypes using the Single Sample Predictor (SSP)	intrinsic.cluster.predict
Function to map a list of datasets through EntrezGene IDs in order to get the union of the genes	map.datasets
Center around the median	medianCtr
Gene modules published in Desmedt et al. 2008	mod1
Gene modules published in Wirapati et al. 2008	mod2
Model used to classify ovarian tumors into Angiogenic and NonAngiogenic subtypes.	modelOvcAngiogenic
Function to identify breast cancer molecular subtypes using the Subtype Clustering Model	molecular.subtyping
Gene expression, annotations and clinical data from van de Vijver et al. 2002	annot.nkis data.nkis demo.nkis nkis
Function to compute the Nottingham Prognostic Index	npi
Function to compute the OncotypeDX signature as published by Paik et al. in 2004.	oncotypedx
Function to compute the subtype scores and risk classifications for the angiogenic molecular subtype in ovarian cancer	ovcAngiogenic
Function to compute the subtype scores and risk classifications for the prognostic signature published by Crinjs et al.	ovcCrijns
Function to compute the prediction scores and risk classifications for the ovarian cancer TCGA signature	ovcTCGA
Function to compute the subtype scores and risk classifications for the prognostic signature published by Yoshihara et al.	ovcYoshihara
Overlap two datasets	overlapSets
PAM50 classifier for identification of breast cancer molecular subtypes (Parker et al 2009)	pam50 pam50.robust pam50.scale
Function to compute the PIK3CA gene signature (PIK3CA-GS)	pik3cags
Function for sample size calculation for correlation coefficients	power.cor
Function to compute the prediction strength of a clustering model	ps.cluster
Function to read a 'csv' file containing gene lists (aka gene signatures)	read.m.file
Overlap two datasets	readArray
Function to rename duplicated strings	rename.duplicate
Function to rescale values based on quantiles	rescale
Function to compute the rorS signature as published by Parker et al 2009	rorS
Subtype Clustering Model using only ESR1, ERBB2 and AURKA genes for identification of breast cancer molecular subtypes	scmgene.robust
Subtype Clustering Model using ESR1, ERBB2 and AURKA modules for identification of breast cancer molecular subtypes (Desmedt et al 2008)	scmod1.robust
Subtype Clustering Model using ESR1, ERBB2 and AURKA modules for identification of breast cancer molecular subtypes (Desmedt et al 2008)	scmod2.robust
Function to set the class of columns in a data.frame	setcolclass.df
Signature used to compute the endoPredict signature as published by Filipits et al 2011	sig.endoPredict
Signature used to compute the 70 genes prognosis profile (GENE70) as published by van't Veer et al. 2002	sig.gene70
Signature used to compute the Relapse Score (GENE76) as published in Wang et al. 2005	sig.gene76
Gene Expression progNostic Index Using Subtypes (GENIUS) as published by Haibe-Kains et al. 2010.	sig.genius
Gene expression Grade Index (GGI) as published in Sotiriou et al. 2006	sig.ggi
Signature used to compute the OncotypeDX signature as published by Paik et al 2004	sig.oncotypedx
Gene expression Grade Index (GGI) as published in Sotiriou et al. 2006	sig.pik3cags
Function to compute signature scores as linear combination of gene expressions	sig.score
Tamoxifen Resistance signature composed of 13 gene clusters (TAMR13) as published by Loi et al. 2008.	sig.tamr13
sigOvcAngiogenic dataset	sigOvcAngiogenic
sigOvcCrijns dataset	sigOvcCrijns
sigOcvSpentzos dataset	sigOvcSpentzos
sigOvcTCGA dataset	sigOvcTCGA
sigOvcYoshihara dataset	sigOvcYoshihara
Function to compute the confidence interval for the Spearman correelation coefficient	spearmanCI
SSP2003 classifier for identification of breast cancer molecular subtypes (Sorlie et al 2003)	ssp2003 ssp2003.robust ssp2003.scale
SSP2006 classifier for identification of breast cancer molecular subtypes (Hu et al 2006)	ssp2006 ssp2006.robust ssp2006.scale
Function to compute the St Gallen consensus criterion for prognostication	st.gallen
Function to quantify stability of feature selection	stab.fs
Function to quantify stability of feature ranking	stab.fs.ranking
Utility function to escape LaTeX special characters present in a string	strescR
Function to fit the Subtype Clustering Model	subtype.cluster
Function to identify breast cancer molecular subtypes using the Subtype Clustering Model	subtype.cluster.predict
Function to compute the risk scores of the tamoxifen resistance signature (TAMR13)	tamr13
Function to compute Tukey's Biweight Robust Mean	tbrm
Gene expression, annotations and clinical data from Wang et al. 2005 and Minn et al 2007	annot.vdxs data.vdxs demo.vdxs vdxs
Function to compute the weighted mean and weighted variance of 'x'	weighted.meanvar
Function to write a 'csv' file containing gene lists (aka gene signatures)	write.m.file

Package: genefu 2.45.0

genefu: Computation of Gene Expression-Based Signatures in Breast Cancer

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