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 |
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.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 |
expos |
Gene expression, annotations and clinical data from the International Genomics Consortium |
fuzzy.ttest |
Function to compute the weighted mean and weighted variance of 'x' |
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) |
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 |
modelOvcAngioganic |
modelOvcAngioganic |
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. |
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) |
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) |
rename.duplicate |
Function to rename duplicated strings. |
rescale |
Function to rescale values based on quantiles |
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) |
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. |
sigAngiogenic |
sigAngiogenic |
sigOvcAngiogenic |
sigOvcAngiogenic |
sigOvcCrijns |
sigOvcCrijns |
sigOvcSpentzos |
sigOvcSpentzos |
sigOvcTCGA |
sigOvcTCGA |
sigOvcYoshihara |
sigOvcYoshihara |
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) |