chimera-package: A package for secondary analysis of fusion products

In chimera: A package for secondary analysis of fusion products

Description

The package imports fusion results from tophat-fusion, tophat-fusion-post, mapSplice, deFuse, fusionmap, bellerophontes, fusionfinder, fusionhunter, STAR, Rsubread, fusionCatcher. The package was design to facilitate the characterisation of fusion products events. Data upload: outputs for the above indicated fusion detection tools can be imported using importFusionData in a list of fSet objects. fSet-class offers various methods to extract information from the fSet objects. The fusion names can be extracted with fusionName function. The number of reads supporting a fusion event cam be extracted with the supportingReads function.

Filtering: The imported fusion list can be filtered using filterList

Annotation: Oncofuse can be installed in chimera with the function oncofuseInstallation Various information on the fusions location, on structural and functional domains affected by the fusion event as well as a prediction of the putative functional effect of the fusion on the cell can be obtained by using oncofuseRun.

chimeraSeqs generates the nucleotide sequence of a fusion transcript described in an fSet object. chimeraSeqSet does the same but on a list of fSet objects.

fusionPeptides allows to investigate if the fusion events generate also a fusion at protein level.

subreadRun allows to remap reads on the fused transcripts reconstructed with chimeraSeqs

Validation GapFiller is a seed-and-extend local assembler capable to produce (in-silico) longer and highly accurate sequences from a collection of Next Generation Sequencing reads. It can be installed in chimera with the function gapfillerInstallation. The function gapfillerRun allows to check if reads mapped by subreadRun over a fused transcript generated with chimeraSeqs are able to reconstruct by de novo assembly the fusion break-point.

Export The function prettyPrint converts the information stored in a list of fSet objects in a dataframe structure that is saved as tab delimited file.

Details

Package:	chimera
Type:	Package
Version:	1.0
Date:	2014-31-07
License:	Artistic-2.0

Author(s)

Raffaele A Calogero Maintainer: Raffaele A Calogero <[e-mail]>

References

Beccuti M, et al. The structure of state-of-art gene fusion-finder algorithms. OA Bioinformatics 2013;1(1):2. Carrara, M., et al. State of art fusion-finder algorithms are suitable to detect transcription-induced chimeras in normal tissues? BMC bioinformatics 2013;14 Suppl 7:S2. Carrara, M., et al. State-of-the-Art Fusion-Finder Algorithms Sensitivity and Specificity. BioMed research international 2013;2013:340620. Shugay, M., et al. Oncofuse: a computational framework for the prediction of the oncogenic potential of gene fusions. Bioinformatics 2013;29(20):2539-2546. Nadalin, F., et al. GapFiller: a de novo assembly approach to fill the gap within paired reads. BMC bioinformatics 2012;13 Suppl 14:S8.

chimera documentation built on Nov. 8, 2020, 5:16 p.m.