Relevant Functions for Gene Expression Analysis, Especially in Breast Cancer.

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Documentation for package ‘genefu’ version 1.0.1

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genefu-package Relevant Functions for Gene Expression Analysis, Especially in Breast Cancer.
annot.nki Gene expression, annotations and clinical data from van de Vijver et al. 2002
annot.vdx 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
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
data.nki Gene expression, annotations and clinical data from van de Vijver et al. 2002
data.vdx Gene expression, annotations and clinical data from Wang et al. 2005 and Minn et al 2007
demo.nki Gene expression, annotations and clinical data from van de Vijver et al. 2002
demo.vdx Gene expression, annotations and clinical data from Wang et al. 2005 and Minn et al 2007
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. 2009
ggi Function to compute the raw and scaled Gene expression Grade Index (GGI)
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
mod1 Gene modules published in Desmedt et al. 2008
mod2 Gene modules published in Wirapati et al. 2008
nki Gene expression, annotations and clinical data from van de Vijver et al. 2002
npi Function to compute the Nottingham Prognostic Index
pam50 PAM50 classifier for identification of breast cancer molecular subtypes (Parker et al 2009)
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)
rescale Function to rescale values based on quantiles
sbtgene Subtype Clustering Model using only ESR1, ERBB2 and AURKA genes for identification of breast cancer molecular subtypes
sbtmod1 Subtype Clustering Model using ESR1, ERBB2 and AURKA modules for identification of breast cancer molecular subtypes (Desmedt et al 2008)
sbtmod2 Subtype Clustering Model using ESR1, ERBB2 and AURKA modules for identification of breast cancer molecular subtypes (Wirapati et al 2008)
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. 2009
sig.ggi 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
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
subtype.cluster Function to fit the Subtype Clustering Model
subtype.cluster.predict Function to identify breast cancer molecular subtypes using the Subtype Clustering Model
tbrm Function to compute Tukey's Biweight Robust Mean
vdx Gene expression, annotations and clinical data from Wang et al. 2005 and Minn et al 2007
write.m.file Function to write a 'csv' file containing gene lists (aka gene signatures)