genefu: Computation of Gene Expression-Based Signatures in Breast Cancer
Version 2.8.0

Description: 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.

AuthorDeena M.A. Gendoo, Natchar Ratanasirigulchai, Markus S. Schroder, Laia Pare, Joel S. Parker, Aleix Prat, and Benjamin Haibe-Kains
Bioconductor views Classification Clustering DifferentialExpression GeneExpression Visualization
Date of publicationNone
MaintainerBenjamin Haibe-Kains <benjamin.haibe.kains@utoronto.ca>, Markus Schroeder <markus.schroeder@ucdconnect.ie>
LicenseArtistic-2.0
Version2.8.0
URL http://www.pmgenomics.ca/bhklab/software/genefu
Package repositoryView on Bioconductor
InstallationInstall the latest version of this package by entering the following in R:
source("https://bioconductor.org/biocLite.R")
biocLite("genefu")

Getting started

Package overview

Popular man pages

gene76: Function to compute the Relapse Score as published by Wang et...
genefu-package: Relevant Functions for Gene Expression Analysis, Especially...
intrinsic.cluster: Function to fit a Single Sample Predictor (SSP) as in Perou,...
molecular.subtyping: Function to identify breast cancer molecular subtypes using...
pam50: PAM50 classifier for identification of breast cancer...
sig.ggi: Gene expression Grade Index (GGI) as published in Sotiriou et...
tbrm: Function to compute Tukey's Biweight Robust Mean
See all...

All man pages Function index File listing

Man pages

bimod: Function to identify bimodality for gene expression or...
boxplotplus2: Box plot of group of values with corresponding jittered...
claudinLow: Claudin-low classification for Breast Cancer Data
claudinLowData: claudinLowData for use in the claudinLow classifier. Data...
collapseIDs: Utility function to collapse IDs
compare.proto.cor: Function to statistically compare correlation to prototypes
compute.pairw.cor.meta: Function to compute pairwise correlations in a...
compute.pairw.cor.z: Function to compute the Z transformation of the pairwise...
compute.proto.cor.meta: Function to compute correlations to prototypes in a...
cordiff.dep: Function to estimate whether two dependent correlations...
endoPredict: Function to compute the endoPredict signature as published by...
expos: Gene expression, annotations and clinical data from the...
fuzzy.ttest: Function to compute the fuzzy Student t test based on...
gene70: Function to compute the 70 genes prognosis profile (GENE70)...
gene76: Function to compute the Relapse Score as published by Wang et...
genefu-package: Relevant Functions for Gene Expression Analysis, Especially...
geneid.map: Function to find the common genes between two datasets or a...
genius: Function to compute the Gene Expression progNostic Index...
ggi: Function to compute the raw and scaled Gene expression Grade...
ihc4: Function to compute the IHC4 prognostic score as published by...
intrinsic.cluster: Function to fit a Single Sample Predictor (SSP) as in Perou,...
intrinsic.cluster.predict: Function to identify breast cancer molecular subtypes using...
map.datasets: Function to map a list of datasets through EntrezGene IDs in...
medianCtr: Center around the median
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...
molecular.subtyping: Function to identify breast cancer molecular subtypes using...
nkis: Gene expression, annotations and clinical data from van de...
npi: Function to compute the Nottingham Prognostic Index
oncotypedx: Function to compute the OncotypeDX signature as published by...
ovcAngiogenic: Function to compute the subtype scores and risk...
ovcCrijns: Function to compute the subtype scores and risk...
ovcTCGA: Function to compute the prediction scores and risk...
ovcYoshihara: Function to compute the subtype scores and risk...
overlapSets: Overlap two datasets
pam50: PAM50 classifier for identification of breast cancer...
pik3cags: Function to compute the PIK3CA gene signature (PIK3CA-GS)
power.cor: Function for sample size calculation for correlation...
ps.cluster: Function to compute the prediction strength of a clustering...
readArray: Overlap two datasets
read.m.file: Function to read a 'csv' file containing gene lists (aka gene...
rename.duplicate: Function to rename duplicated strings.
rescale: Function to rescale values based on quantiles
rorS: Function to compute the rorS signature as published by Parker...
scmgene.robust: Subtype Clustering Model using only ESR1, ERBB2 and AURKA...
scmod1.robust: Subtype Clustering Model using ESR1, ERBB2 and AURKA modules...
scmod2.robust: Subtype Clustering Model using ESR1, ERBB2 and AURKA modules...
setcolclass.df: Function to set the class of columns in a data.frame
sig.endoPredict: Signature used to compute the endoPredict signature as...
sig.gene70: Signature used to compute the 70 genes prognosis profile...
sig.gene76: Signature used to compute the Relapse Score (GENE76) as...
sig.genius: Gene Expression progNostic Index Using Subtypes (GENIUS) as...
sig.ggi: Gene expression Grade Index (GGI) as published in Sotiriou et...
sig.oncotypedx: Signature used to compute the OncotypeDX signature as...
sigOvcAngiogenic: a
sigOvcCrijns: a
sigOvcSpentzos: a
sigOvcTCGA: a
sigOvcYoshihara: a
sig.pik3cags: Gene expression Grade Index (GGI) as published in Sotiriou et...
sig.score: Function to compute signature scores as linear combination of...
sig.tamr13: Tamoxifen Resistance signature composed of 13 gene clusters...
spearmanCI: Function to compute the confidence interval for the Spearman...
ssp2003: SSP2003 classifier for identification of breast cancer...
ssp2006: SSP2006 classifier for identification of breast cancer...
stab.fs: Function to quantify stability of feature selection.
stab.fs.ranking: Function to quantify stability of feature ranking.
st.gallen: Function to compute the St Gallen consensus criterion for...
strescR: Utility function to escape LaTeX special characters present...
subtype.cluster: Function to fit the Subtype Clustering Model
subtype.cluster.predict: Function to identify breast cancer molecular subtypes using...
tamr13: Function to compute the risk scores of the tamoxifen...
tbrm: Function to compute Tukey's Biweight Robust Mean
vdxs: Gene expression, annotations and clinical data from Wang et...
weighted.meanvar: Function to compute the weighted mean and weighted variance...
write.m.file: Function to write a 'csv' file containing gene lists (aka...

Functions

annot.expos Man page
annot.nkis Man page
annot.vdxs Man page
bimod Man page
boxplotplus2 Man page
claudinLow Man page Source code
claudinLowData Man page
collapseIDs Man page Source code
compare.proto.cor Man page
compute.pairw.cor.meta Man page
compute.pairw.cor.z Man page
compute.proto.cor.meta Man page
cordiff.dep Man page
data.expos Man page
data.nkis Man page
data.vdxs Man page
demo.expos Man page
demo.nkis Man page
demo.vdxs Man page
endoPredict Man page
expos Man page
fuzzy.ttest Man page
gene70 Man page
gene76 Man page
genefu Man page
genefu-package Man page
geneid.map Man page
genius Man page
ggi Man page
ihc4 Man page
intrinsic.cluster Man page
intrinsic.cluster.predict Man page
map.datasets Man page
medianCtr Man page Source code
mod1 Man page
mod2 Man page
modelOvcAngiogenic Man page
molecular.subtyping Man page Source code
nkis Man page
npi Man page
oncotypedx Man page
ovcAngiogenic Man page
ovcCrijns Man page
ovcTCGA Man page
ovcYoshihara Man page
overlapSets Man page Source code
pam50 Man page
pam50.robust Man page
pam50.scale Man page
pik3cags Man page
power.cor Man page
ps.cluster Man page
read.m.file Man page
readArray Man page
readarray Source code
rename.duplicate Man page
rescale Man page
rorS Man page
scmgene.robust Man page
scmod1.robust Man page
scmod2.robust Man page
setcolclass.df Man page
sig.endoPredict Man page
sig.gene70 Man page
sig.gene76 Man page
sig.genius Man page
sig.ggi Man page
sig.oncotypedx Man page
sig.pik3cags Man page
sig.score Man page
sig.tamr13 Man page
sigOvcAngiogenic Man page
sigOvcCrijns Man page
sigOvcSpentzos Man page
sigOvcTCGA Man page
sigOvcYoshihara Man page
spearmanCI Man page
ssp2003 Man page
ssp2003.robust Man page
ssp2003.scale Man page
ssp2006 Man page
ssp2006.robust Man page
ssp2006.scale Man page
st.gallen Man page
stab.fs Man page
stab.fs.ranking Man page
strescR Man page
subtype.cluster Man page
subtype.cluster.predict Man page
tamr13 Man page
tbrm Man page
vdxs Man page
weighted.meanvar Man page
write.m.file Man page

Files

DESCRIPTION
NAMESPACE
R
R/SpearmanCI.R
R/bimod.R
R/boxplotplus2.R
R/claudinLow.R
R/collapseIDs.R
R/compare.proto.cor.R
R/compute.pairw.cor.meta.R
R/compute.pairw.cor.z.R
R/compute.proto.cor.meta.R
R/cordiff.dep.R
R/endoPredict.R
R/fuzzy.ttest.R
R/gene70.R
R/gene76.R
R/geneid.map.R
R/genius.R
R/ggi.R
R/ihc4.R
R/intrinsic.cluster.R
R/intrinsic.cluster.predict.R
R/map.datasets.R
R/medianCtr.R
R/molecular.subtyping.R
R/npi.R
R/oncotypedx.R
R/ovcAngiogenic.R
R/ovcCrijns.R
R/ovcSigs.R
R/ovcTCGA.R
R/ovcYoshihara.R
R/overlapSets.R
R/pik3cags.R
R/power.cor.R
R/ps.cluster.R
R/read.m.file.R
R/readArray.R
R/rename.duplicate.R
R/rescale.R
R/rorS.R
R/setcolclass.df.R
R/sig.score.R
R/st.gallen.R
R/stab.fs.R
R/stab.fs.ranking.R
R/strescR.R
R/subtype.cluster.R
R/subtype.cluster.predict.R
R/tamr13.R
R/tbrm.R
R/weighted.meanvar.R
R/write.m.file.R
README
build
build/genefu.pdf
build/vignette.rds
data
data/claudinLowData.rda
data/datalist
data/expos.rda
data/mod1.rda
data/mod2.rda
data/modelOvcAngiogenic.rda
data/nkis.rda
data/pam50.rda
data/pam50.robust.rda
data/pam50.scale.rda
data/scmgene.robust.rda
data/scmod1.robust.rda
data/scmod2.robust.rda
data/sig.endoPredict.rda
data/sig.gene70.rda
data/sig.gene76.rda
data/sig.genius.rda
data/sig.ggi.rda
data/sig.oncotypedx.rda
data/sig.pik3cags.rda
data/sig.tamr13.rda
data/sigOvcAngiogenic.rda
data/sigOvcCrijns.rda
data/sigOvcSpentzos.rda
data/sigOvcTCGA.rda
data/sigOvcYoshihara.rda
data/ssp2003.rda
data/ssp2003.robust.rda
data/ssp2003.scale.rda
data/ssp2006.rda
data/ssp2006.robust.rda
data/ssp2006.scale.rda
data/vdxs.rda
inst
inst/doc
inst/doc/genefu.R
inst/doc/genefu.Rnw
inst/doc/genefu.pdf
inst/extdata
inst/extdata/T.E.9CELL-LINE.txt
inst/extdata/bentink2012_angiogenic.csv
inst/extdata/crijns2009_sig.csv
inst/extdata/desmedt2008_genemodules.csv
inst/extdata/filipits2011_sig_endopredict.csv
inst/extdata/haibekains2009_sig_genius.csv
inst/extdata/loi2008_tamr13.csv
inst/extdata/loi2010_pik3cags.csv
inst/extdata/paik2004_sig_oncotypedx.csv
inst/extdata/pam50_model.csv
inst/extdata/scmgene_robust_model.csv
inst/extdata/scmod1_robust_model.csv
inst/extdata/scmod2_robust_model.csv
inst/extdata/sotiriou2006_sig_ggi.csv
inst/extdata/spentzos2011_sig.csv
inst/extdata/ssp2003_model.csv
inst/extdata/ssp2006_model.csv
inst/extdata/tcga2011_sig.csv
inst/extdata/veer2002_sig_gene70.csv
inst/extdata/wang2005_sig_gene76.csv
inst/extdata/wirapati2008_genemodules.csv
inst/extdata/yoshihara2010_sig.csv
man
man/bimod.Rd
man/boxplotplus2.Rd
man/claudinLow.Rd
man/claudinLowData.Rd
man/collapseIDs.Rd
man/compare.proto.cor.Rd
man/compute.pairw.cor.meta.Rd
man/compute.pairw.cor.z.Rd
man/compute.proto.cor.meta.Rd
man/cordiff.dep.Rd
man/endoPredict.Rd
man/expos.Rd
man/fuzzy.ttest.Rd
man/gene70.Rd
man/gene76.Rd
man/genefu-package.Rd
man/geneid.map.Rd
man/genius.Rd
man/ggi.Rd
man/ihc4.Rd
man/intrinsic.cluster.Rd
man/intrinsic.cluster.predict.Rd
man/map.datasets.Rd
man/medianCtr.Rd
man/mod1.Rd
man/mod2.Rd
man/modelOvcAngiogenic.Rd
man/molecular.subtyping.Rd
man/nkis.Rd
man/npi.Rd
man/oncotypedx.Rd
man/ovcAngiogenic.Rd
man/ovcCrijns.Rd
man/ovcTCGA.Rd
man/ovcYoshihara.Rd
man/overlapSets.Rd
man/pam50.Rd
man/pik3cags.Rd
man/power.cor.Rd
man/ps.cluster.Rd
man/read.m.file.Rd
man/readArray.Rd
man/rename.duplicate.Rd
man/rescale.Rd
man/rorS.Rd
man/scmgene.robust.Rd
man/scmod1.robust.Rd
man/scmod2.robust.Rd
man/setcolclass.df.Rd
man/sig.endoPredict.Rd
man/sig.gene70.Rd
man/sig.gene76.Rd
man/sig.genius.Rd
man/sig.ggi.Rd
man/sig.oncotypedx.Rd
man/sig.pik3cags.Rd
man/sig.score.Rd
man/sig.tamr13.Rd
man/sigOvcAngiogenic.Rd
man/sigOvcCrijns.Rd
man/sigOvcSpentzos.Rd
man/sigOvcTCGA.Rd
man/sigOvcYoshihara.Rd
man/spearmanCI.Rd
man/ssp2003.Rd
man/ssp2006.Rd
man/st.gallen.Rd
man/stab.fs.Rd
man/stab.fs.ranking.Rd
man/strescR.Rd
man/subtype.cluster.Rd
man/subtype.cluster.predict.Rd
man/tamr13.Rd
man/tbrm.Rd
man/vdxs.Rd
man/weighted.meanvar.Rd
man/write.m.file.Rd
vignettes
vignettes/genefu.Rnw
genefu documentation built on May 20, 2017, 10:32 p.m.