A package for secondary analysis of fusion products


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Documentation for package ‘chimera’ version 1.8.5

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chimera-package A package for secondary analysis of fusion products
addGA Class fSet, a class represent fusion data, and methods for processing it
addGA-method Class fSet, a class represent fusion data, and methods for processing it
addRNA Class fSet, a class represent fusion data, and methods for processing it
addRNA-method Class fSet, a class represent fusion data, and methods for processing it
bam2fastq A function to extract pair end reads from the bam file generated with subreadRun function
breakpointOverlaps A function to extract the reads overlapping to fusion breakpoint.
chimera A package for secondary analysis of fusion products
chimeraSeqs A function to generate the nucleotide sequences of a fusion event
chimeraSeqSet A function to generates DNAStringSet encompassing fusion sequences
defuseTPTN A function that genererate a list of fSet objects encopassing 60 experimentally validated fusions and 61 false fusions
filterList A function to filter a list of fSet objects
filterSamReads A function to filter SAM or BAM files
fSet Class fSet, a class represent fusion data, and methods for processing it
fSet-class Class fSet, a class represent fusion data, and methods for processing it
fusionData Class fSet, a class represent fusion data, and methods for processing it
fusionData-method Class fSet, a class represent fusion data, and methods for processing it
fusionGA Class fSet, a class represent fusion data, and methods for processing it
fusionGA-method Class fSet, a class represent fusion data, and methods for processing it
fusionGRL Class fSet, a class represent fusion data, and methods for processing it
fusionGRL-method Class fSet, a class represent fusion data, and methods for processing it
fusionName A function to extract fusion names for a list of fSet object
fusionPeptides A function to investigate the peptides involved in the fusion event.
fusionRNA Class fSet, a class represent fusion data, and methods for processing it
fusionRNA-method Class fSet, a class represent fusion data, and methods for processing it
gapfillerInstallation A function to download a compiled version of GapFiller
gapfillerRun A function to confirm fusion break point by de novo assembly
gapfillerWrap A function to prepare files and to run gapfiller
importFusionData A function to import fusion data detected by different fusion finders
is.fSet A function to evaulate if an object belongs to fSet class or not
MHmakeRandomString A function generating a random string
newfSet A constructor for fSet class objects
newfSet-method Class fSet, a class represent fusion data, and methods for processing it
oncofuseInstallation A function to download oncofuse
oncofuseRun A function to annotate fusions with Oncofuse. Oncofuse is a naive bayesian classifier. Its goal is to identify those fusion sequences with higher probability of being driver than passenger events
picardInstallation A function to download picard-tools
plotCoverage A function to plot the coverage of a fusion gene
prettyPrint A function to represent a list of fSet as a dataframe
removingErrorLine A function to remove a line stopping SAM to BAM conversion
starInstallation A function to download STAR
starReads A function to extract reads info from STAR fusion output
starRun A function to generate a bam file for fusions coverage evaluation
subreadRun A function to generate a bam file for fusions coverage evaluation
supportingReads A function to extract supporting reads values from a list of fSet object
tophatInstallation A function to download tophat, bowtie and samtools
tophatRun A function to generate a bam file for fusions coverage evaluation
validateSamFile A function to validate SAM or BAM files