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
compare.proto.cor       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
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-package          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)
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)
ssp2006                 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)
