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genefu (version 2.4.2)

Computation of Gene Expression-Based Signatures in Breast Cancer

Description

This package contains functions implementing various tasks usually required by gene expression analysis, especially in breast cancer studies: gene mapping between different microarray platforms, identification of molecular subtypes, implementation of published gene signatures, gene selection, and survival analysis.

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Monthly Downloads

12

Version

2.4.2

License

Artistic-2.0

Maintainer

Benjamin HaibeKains

Last Published

February 15th, 2017

Functions in genefu (2.4.2)

Function to estimate whether two dependent correlations differ

PAM50 classifier for identification of breast cancer molecular subtypes (Parker et al 2009)

Tamoxifen Resistance signature composed of 13 gene clusters (TAMR13) as published by Loi et al. 2008.

Function to identify bimodality for gene expression or signature score

rename.duplicate

Function to rename duplicated strings.

compare.proto.cor

Function to statistically compare correlation to prototypes

Gene Expression progNostic Index Using Subtypes (GENIUS) as published by Haibe-Kains et al. 2010.

Overlap two datasets

Function to compute the St Gallen consensus criterion for prognostication

Function to set the class of columns in a data.frame

Gene expression, annotations and clinical data from van de Vijver et al. 2002

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

Function to compute the Relapse Score as published by Wang et al. 2005

Function to compute the PIK3CA gene signature (PIK3CA-GS)

Function to compute the subtype scores and risk classifications for the prognostic signature published by Yoshihara et al.

compute.proto.cor.meta

Function to compute correlations to prototypes in a meta-analytical framework

Signature used to compute the 70 genes prognosis profile (GENE70) as published by van't Veer et al. 2002

modelOvcAngiogenic

Model used to classify ovarian tumors into Angiogenic and NonAngiogenic subtypes.

Signature used to compute the OncotypeDX signature as published by Paik et al 2004

Function to rescale values based on quantiles

sig.endoPredict

Signature used to compute the endoPredict signature as published by Filipits et al 2011

Function to compute the rorS signature as published by Parker et al 2009

Function to quantify stability of feature selection.

Function to compute the subtype scores and risk classifications for the prognostic signature published by Crinjs et al.

Function to compute the risk scores of the tamoxifen resistance signature (TAMR13)

weighted.meanvar

Function to compute the weighted mean and weighted variance of 'x'

Subtype Clustering Model using only ESR1, ERBB2 and AURKA genes for identification of breast cancer molecular subtypes

SSP2006 classifier for identification of breast cancer molecular subtypes (Hu et al 2006)

Box plot of group of values with corresponding jittered points

stab.fs.ranking

Function to quantify stability of feature ranking.

Function to write a 'csv' file containing gene lists (aka gene signatures)

compute.pairw.cor.z

Function to compute the Z transformation of the pairwise correlations for a list of datasets

Function to compute the endoPredict signature as published by Filipits et al 2011

compute.pairw.cor.meta

Function to compute pairwise correlations in a meta-analytical framework

Function to compute the 70 genes prognosis profile (GENE70) as published by van't Veer et al. 2002

Subtype Clustering Model using ESR1, ERBB2 and AURKA modules for identification of breast cancer molecular subtypes (Wirapati et al 2008)

Function to compute the confidence interval for the Spearman correelation coefficient

Function to compute signature scores as linear combination of gene expressions

subtype.cluster

Function to fit the Subtype Clustering Model

Center around the median

Gene modules published in Wirapati et al. 2008

Function to find the common genes between two datasets or a dataset and a gene list

Function to compute the subtype scores and risk classifications for the angiogenic molecular subtype in ovarian cancer

Subtype Clustering Model using ESR1, ERBB2 and AURKA modules for identification of breast cancer molecular subtypes (Desmedt et al 2008)

Gene expression Grade Index (GGI) as published in Sotiriou et al. 2006

Function to compute the raw and scaled Gene expression Grade Index (GGI)

Function to compute the OncotypeDX signature as published by Paik et al. in 2004.

Function to compute the prediction scores and risk classifications for the ovarian cancer TCGA signature

Overlap two datasets

subtype.cluster.predict

Function to identify breast cancer molecular subtypes using the Subtype Clustering Model

Gene expression, annotations and clinical data from Wang et al. 2005 and Minn et al 2007

Function to compute Tukey's Biweight Robust Mean

claudinLowData for use in the claudinLow classifier. Data generously provided by Aleix Prat.

Function to compute the Nottingham Prognostic Index

Function to read a 'csv' file containing gene lists (aka gene signatures)

Signature used to compute the Relapse Score (GENE76) as published in Wang et al. 2005

Function to compute the prediction strength of a clustering model

intrinsic.cluster.predict

Function to identify breast cancer molecular subtypes using the Single Sample Predictor (SSP)

Function to compute the fuzzy Student t test based on weighted mean and weighted variance

Gene modules published in Desmedt et al. 2008

Function to map a list of datasets through EntrezGene IDs in order to get the union of the genes

Gene expression Grade Index (GGI) as published in Sotiriou et al. 2006

sigOvcYoshihara

Gene expression, annotations and clinical data from the International Genomics Consortium

SSP2003 classifier for identification of breast cancer molecular subtypes (Sorlie et al 2003)

Utility function to collapse IDs

Function to compute the Gene Expression progNostic Index Using Subtypes (GENIUS) as published by Haibe-Kains et al. 2010

Claudin-low classification for Breast Cancer Data

molecular.subtyping

Function to identify breast cancer molecular subtypes using the Subtype Clustering Model

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

Function for sample size calculation for correlation coefficients

sigOvcAngiogenic

Utility function to escape LaTeX special characters present in a string