Computation of Gene Expression-Based Signatures in Breast Cancer

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Documentation for package ‘genefu’ version 2.40.0

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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
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 (Desmedt 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 sigOvcAngiogenic dataset
sigOvcCrijns sigOvcCrijns dataset
sigOvcSpentzos sigOcvSpentzos dataset
sigOvcTCGA sigOvcTCGA dataset
sigOvcYoshihara sigOvcYoshihara dataset
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)