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

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.

Author
Deena M.A. Gendoo, Natchar Ratanasirigulchai, Markus S. Schroder, Laia Pare, Joel S. Parker, Aleix Prat, and Benjamin Haibe-Kains
Date of publication
None
Maintainer
Benjamin Haibe-Kains <benjamin.haibe.kains@utoronto.ca>, Markus Schroeder <markus.schroeder@ucdconnect.ie>
License
Artistic-2.0
Version
2.6.0
URLs

View on Bioconductor

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...

Files in this package

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