Man pages for Bioconductor-mirror/genefu
Computation of Gene Expression-Based Signatures in Breast Cancer

bimodFunction to identify bimodality for gene expression or...
boxplotplus2Box plot of group of values with corresponding jittered...
claudinLowClaudin-low classification for Breast Cancer Data
claudinLowDataclaudinLowData for use in the claudinLow classifier. Data...
collapseIDsUtility function to collapse IDs
compare.proto.corFunction to statistically compare correlation to prototypes
compute.pairw.cor.metaFunction to compute pairwise correlations in a...
compute.pairw.cor.zFunction to compute the Z transformation of the pairwise...
compute.proto.cor.metaFunction to compute correlations to prototypes in a...
cordiff.depFunction to estimate whether two dependent correlations...
endoPredictFunction to compute the endoPredict signature as published by...
exposGene expression, annotations and clinical data from the...
fuzzy.ttestFunction to compute the fuzzy Student t test based on...
gene70Function to compute the 70 genes prognosis profile (GENE70)...
gene76Function to compute the Relapse Score as published by Wang et...
genefu-packageRelevant Functions for Gene Expression Analysis, Especially...
geneid.mapFunction to find the common genes between two datasets or a...
geniusFunction to compute the Gene Expression progNostic Index...
ggiFunction to compute the raw and scaled Gene expression Grade...
ihc4Function to compute the IHC4 prognostic score as published by...
intrinsic.clusterFunction to fit a Single Sample Predictor (SSP) as in Perou,...
intrinsic.cluster.predictFunction to identify breast cancer molecular subtypes using...
map.datasetsFunction to map a list of datasets through EntrezGene IDs in...
medianCtrCenter around the median
mod1Gene modules published in Desmedt et al. 2008
mod2Gene modules published in Wirapati et al. 2008
modelOvcAngiogenicModel used to classify ovarian tumors into Angiogenic and...
molecular.subtypingFunction to identify breast cancer molecular subtypes using...
nkisGene expression, annotations and clinical data from van de...
npiFunction to compute the Nottingham Prognostic Index
oncotypedxFunction to compute the OncotypeDX signature as published by...
ovcAngiogenicFunction to compute the subtype scores and risk...
ovcCrijnsFunction to compute the subtype scores and risk...
ovcTCGAFunction to compute the prediction scores and risk...
ovcYoshiharaFunction to compute the subtype scores and risk...
overlapSetsOverlap two datasets
pam50PAM50 classifier for identification of breast cancer...
pik3cagsFunction to compute the PIK3CA gene signature (PIK3CA-GS)
power.corFunction for sample size calculation for correlation...
ps.clusterFunction to compute the prediction strength of a clustering...
readArrayOverlap two datasets
read.m.fileFunction to read a 'csv' file containing gene lists (aka gene...
rename.duplicateFunction to rename duplicated strings.
rescaleFunction to rescale values based on quantiles
rorSFunction to compute the rorS signature as published by Parker...
scmgene.robustSubtype Clustering Model using only ESR1, ERBB2 and AURKA...
scmod1.robustSubtype Clustering Model using ESR1, ERBB2 and AURKA modules...
scmod2.robustSubtype Clustering Model using ESR1, ERBB2 and AURKA modules...
setcolclass.dfFunction to set the class of columns in a data.frame
sig.endoPredictSignature used to compute the endoPredict signature as...
sig.gene70Signature used to compute the 70 genes prognosis profile...
sig.gene76Signature used to compute the Relapse Score (GENE76) as...
sig.geniusGene Expression progNostic Index Using Subtypes (GENIUS) as...
sig.ggiGene expression Grade Index (GGI) as published in Sotiriou et...
sig.oncotypedxSignature used to compute the OncotypeDX signature as...
sigOvcAngiogenica
sigOvcCrijnsa
sigOvcSpentzosa
sigOvcTCGAa
sigOvcYoshiharaa
sig.pik3cagsGene expression Grade Index (GGI) as published in Sotiriou et...
sig.scoreFunction to compute signature scores as linear combination of...
sig.tamr13Tamoxifen Resistance signature composed of 13 gene clusters...
spearmanCIFunction to compute the confidence interval for the Spearman...
ssp2003SSP2003 classifier for identification of breast cancer...
ssp2006SSP2006 classifier for identification of breast cancer...
stab.fsFunction to quantify stability of feature selection.
stab.fs.rankingFunction to quantify stability of feature ranking.
st.gallenFunction to compute the St Gallen consensus criterion for...
strescRUtility function to escape LaTeX special characters present...
subtype.clusterFunction to fit the Subtype Clustering Model
subtype.cluster.predictFunction to identify breast cancer molecular subtypes using...
tamr13Function to compute the risk scores of the tamoxifen...
tbrmFunction to compute Tukey's Biweight Robust Mean
vdxsGene expression, annotations and clinical data from Wang et...
weighted.meanvarFunction to compute the weighted mean and weighted variance...
write.m.fileFunction to write a 'csv' file containing gene lists (aka...
Bioconductor-mirror/genefu documentation built on June 1, 2017, 9:40 a.m.