supportingReads
(Package: chimera) :
A function to extract supporting reads values from a list of fSet object
A function extracting supporting reads values from a list of fSet objects. Please note that not all outputs of supported tools provides both spanning reads, i.e. pair-end reads having one of the two mates spanning over the break point, and encompassing reads, i.e. pair-end reads having the two mates mapping on the exons of the two transcripts involved in the fusion. The presence of both type of reads is mandatory to provide the full number of reads covering the junction region. To know which information are provided by the supported tool please check fSet
● Data Source:
BioConductor
● Keywords: utilities
● Alias: supportingReads
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tophatInstallation
(Package: chimera) :
A function to download tophat, bowtie and samtools
A function allowing the download and installation of tophat, bowtie and samtools in chimera package folder. The function also creates soft links in the user bin folder to allow the call of the above mentioned programs.
● Data Source:
BioConductor
● Keywords: utilities
● Alias: tophatInstallation
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tophatRun
(Package: chimera) :
A function to generate a bam file for fusions coverage evaluation
A function mapping reads to a chimera sequence set. The bam produced by this remapping on a putative fusion will be used to plot the coverage data for all the fused constructs. The function assumes that tophat is installed and located in the path. To run TopHat a softlink to bowtie or bowtie2 need to located in the user bin dir
● Data Source:
BioConductor
● Keywords: utilities
● Alias: tophatRun
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validateSamFile
(Package: chimera) :
A function to validate SAM or BAM files
A function to validate SAM or BAM files using picard-tools
● Data Source:
BioConductor
● Keywords: utilities
● Alias: validateSamFile
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MHmakeRandomString
(Package: chimera) :
A function generating a random string
A function generating a random string.
● Data Source:
BioConductor
● Keywords: utilities
● Alias: MHmakeRandomString
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bam2fastq
(Package: chimera) :
A function to extract pair end reads from the bam file generated with subreadRun function
A function to extract pair end reads from the bam file generated with subread function. The output files are ready to be used for fusion validation with gapfiller
● Data Source:
BioConductor
● Keywords: utilities
● Alias: bam2fastq
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breakpointOverlaps
(Package: chimera) :
A function to extract the reads overlapping to fusion breakpoint.
A function to extract the reads overlapping to fusion breakpoint.
● Data Source:
BioConductor
● Keywords: utilities
● Alias: breakpointOverlaps
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chimera-package
(Package: chimera) :
A package for secondary analysis of fusion products
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.
● Data Source:
BioConductor
● Keywords: package
● Alias: chimera, chimera-package
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chimeraSeqSet
(Package: chimera) :
A function to generates DNAStringSet encompassing fusion sequences
A function generating the nucleotide sequences of chimeras described in a list of fSet, i.e. the list generated using importFusionData function.
● Data Source:
BioConductor
● Keywords: utilities
● Alias: chimeraSeqSet
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chimeraSeqs
(Package: chimera) :
A function to generate the nucleotide sequences of a fusion event
A function generating the nucleotide sequences of a chimera.
● Data Source:
BioConductor
● Keywords: utilities
● Alias: chimeraSeqs
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