# Computation of Gene Expression-Based Signatures in Breast Cancer

## Documentation for package ‘genefu’ version 2.16.0

- DESCRIPTION file.
- User guides, package vignettes and other documentation.

## Help Pages

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