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- genefu: Computation of Gene Expression-Based Signatures in Breast Cancer
- sigOvcTCGA: a
a
Description
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Usage
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Format
sigOvcTCGA
a.
References
Bell D, Berchuck A, Birrer M et al. (2011) "Integrated genomic analyses of ovarian carcinoma", Nature, 474(7353):609–615
Examples
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- bimod: Function to identify bimodality for gene expression or...
- boxplotplus2: Box plot of group of values with corresponding jittered...
- claudinLow: Claudin-low classification for Breast Cancer Data
- claudinLowData: claudinLowData for use in the claudinLow classifier. Data...
- 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...
- compute.pairw.cor.z: Function to compute the Z transformation of the pairwise...
- compute.proto.cor.meta: Function to compute correlations to prototypes in a...
- cordiff.dep: Function to estimate whether two dependent correlations...
- endoPredict: Function to compute the endoPredict signature as published by...
- expos: Gene expression, annotations and clinical data from the...
- fuzzy.ttest: Function to compute the fuzzy Student t test based on...
- gene70: Function to compute the 70 genes prognosis profile (GENE70)...
- gene76: Function to compute the Relapse Score as published by Wang et...
- genefu-package: Relevant Functions for Gene Expression Analysis, Especially...
- geneid.map: Function to find the common genes between two datasets or a...
- genius: Function to compute the Gene Expression progNostic Index...
- ggi: Function to compute the raw and scaled Gene expression Grade...
- ihc4: Function to compute the IHC4 prognostic score as published by...
- intrinsic.cluster: Function to fit a Single Sample Predictor (SSP) as in Perou,...
- intrinsic.cluster.predict: Function to identify breast cancer molecular subtypes using...
- map.datasets: Function to map a list of datasets through EntrezGene IDs in...
- 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...
- molecular.subtyping: Function to identify breast cancer molecular subtypes using...
- nkis: Gene expression, annotations and clinical data from van de...
- npi: Function to compute the Nottingham Prognostic Index
- oncotypedx: Function to compute the OncotypeDX signature as published by...
- ovcAngiogenic: Function to compute the subtype scores and risk...
- ovcCrijns: Function to compute the subtype scores and risk...
- ovcTCGA: Function to compute the prediction scores and risk...
- ovcYoshihara: Function to compute the subtype scores and risk...
- overlapSets: Overlap two datasets
- pam50: PAM50 classifier for identification of breast cancer...
- pik3cags: Function to compute the PIK3CA gene signature (PIK3CA-GS)
- power.cor: Function for sample size calculation for correlation...
- ps.cluster: Function to compute the prediction strength of a clustering...
- readArray: Overlap two datasets
- read.m.file: Function to read a 'csv' file containing gene lists (aka gene...
- 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...
- scmgene.robust: Subtype Clustering Model using only ESR1, ERBB2 and AURKA...
- scmod1.robust: Subtype Clustering Model using ESR1, ERBB2 and AURKA modules...
- scmod2.robust: Subtype Clustering Model using ESR1, ERBB2 and AURKA modules...
- setcolclass.df: Function to set the class of columns in a data.frame
- sig.endoPredict: Signature used to compute the endoPredict signature as...
- sig.gene70: Signature used to compute the 70 genes prognosis profile...
- sig.gene76: Signature used to compute the Relapse Score (GENE76) as...
- sig.genius: Gene Expression progNostic Index Using Subtypes (GENIUS) as...
- sig.ggi: Gene expression Grade Index (GGI) as published in Sotiriou et...
- sig.oncotypedx: Signature used to compute the OncotypeDX signature as...
- sigOvcAngiogenic: a
- sigOvcCrijns: a
- sigOvcSpentzos: a
- sigOvcTCGA: a
- sigOvcYoshihara: a
- sig.pik3cags: Gene expression Grade Index (GGI) as published in Sotiriou et...
- sig.score: Function to compute signature scores as linear combination of...
- sig.tamr13: Tamoxifen Resistance signature composed of 13 gene clusters...
- spearmanCI: Function to compute the confidence interval for the Spearman...
- ssp2003: SSP2003 classifier for identification of breast cancer...
- ssp2006: SSP2006 classifier for identification of breast cancer...
- stab.fs: Function to quantify stability of feature selection.
- stab.fs.ranking: Function to quantify stability of feature ranking.
- st.gallen: Function to compute the St Gallen consensus criterion for...
- strescR: Utility function to escape LaTeX special characters present...
- subtype.cluster: Function to fit the Subtype Clustering Model
- subtype.cluster.predict: Function to identify breast cancer molecular subtypes using...
- tamr13: Function to compute the risk scores of the tamoxifen...
- tbrm: Function to compute Tukey's Biweight Robust Mean
- vdxs: Gene expression, annotations and clinical data from Wang et...
- weighted.meanvar: Function to compute the weighted mean and weighted variance...
- write.m.file: Function to write a 'csv' file containing gene lists (aka...