GenRank : A R/Bioconductor package for prioritization of candidate genes

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http://hdl.handle.net/10138/299328

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Kanduri , C & Järvelä , I 2017 , ' GenRank : A R/Bioconductor package for prioritization of candidate genes ' , F1000Research , vol. 6 , 463 . https://doi.org/10.12688/f1000research.11223.1

Titel: GenRank : A R/Bioconductor package for prioritization of candidate genes
Författare: Kanduri, C.; Järvelä, I.
Upphovmannens organisation: Irma Järvelä / Principal Investigator
Department of Medical and Clinical Genetics
Medicum
University of Helsinki
Datum: 2017
Språk: eng
Sidantal: 9
Tillhör serie: F1000Research
ISSN: 2046-1402
DOI: https://doi.org/10.12688/f1000research.11223.1
Permanenta länken (URI): http://hdl.handle.net/10138/299328
Abstrakt: Modern high-throughput studies often yield long lists of genes, a fraction of which are of high relevance to the phenotype of interest. To prioritize the candidate genes of complex genetic traits, our R/Bioconductor package GenRank ranks genes based on convergent evidence obtained from multiple layers of independent evidence. We implemented three methods to rank genes that integrate gene-level data generated from multiple layers of evidence: (a) the convergent evidence (CE) method aggregates evidence based on a weighted vote counting method; (b) the rank product (RP) method performs a meta-analysis of microarray-based gene expression data, and (c) the traditional method combines p-values. The methods are implemented in R and are available as a package in the Bioconductor repository. (http://bioconductor.org/packages/GenRank/). © 2017 Kanduri C and Järvelä I.
Subject: Article
convergent evidence evidence
data analysis software
gene expression
genetic trait
genetic variation
methodology
rank product method
statistical significance
3111 Biomedicine
1184 Genetics, developmental biology, physiology
Referentgranskad: Ja
Användningsbegränsning: openAccess
Parallelpublicerad version: publishedVersion


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