Article

PLRS: a flexible tool for the joint analysis of DNA copy number and mRNA expression data

Department of Mathematics, VU University, De Boelelaan 1081a, 1081HV Amsterdam, The Netherlands.
Bioinformatics (Impact Factor: 4.62). 02/2013; 29(8). DOI: 10.1093/bioinformatics/btt082
Source: PubMed

ABSTRACT DNA copy number and mRNA expression are commonly used data types in cancer studies. Available software for integrative analysis arbitrarily fixes the parametric form of the association between the two molecular levels and hence offers no opportunities for modeling it. We present a new tool for flexible modeling of this association. PLRS employs a wide class of interpretable models including popular ones and incorporates prior biological knowledge. It is capable to identify the gene-specific type of relationship between gene copy number and mRNA expression. Moreover, it tests the strength of the association and provides confidence intervals. We illustrate PLRS using glioblastoma data from The Cancer Genome Atlas (TCGA). AVAILABILITY: PLRS is implemented as an R package and available from Bioconductor (as of version 2.12; http://bioconductor.org). Additional code for parallel computations is available as Supplementary Material. CONTACT: g.g.r.leday@vu.nl.

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