General Information
| Description | A flexible tool for the joint analysis of DNA copy number and mRNA expression data |
| Homepage | http://bioconductor.org |
Publications
PLRS: a flexible tool for the joint analysis of DNA copy number and mRNA expression data
Summary:
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 modelling it. We present a new tool for flexible modelling of this association. PLRS uses 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.
Availability and implementation:
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
Supplementary information:
Supplementary data are available at Bioinformatics online.
Related Tools
DR-Integrator
Published December 2009
A new analytic tool for integrating DNA copy number and gene expression data
BACOM
Published April 2011
In silico detection of genomic deletion types and correction of normal cell contamination in copy number data
CNAmet
Published January 2011
An R package for integrating copy number, methylation and expression data
WaveCNV
Published November 2013
Allele-specific copy number alterations in primary tumors and xenograft models from next-generation sequencing
PINCAGE
Published January 2016
Probabilistic integration of cancer genomics data for perturbed gene identification and sample classification
FAIR Evaluation
Sorry, you must be signed in to evaluate this object.
