# A package for secondary analysis of fusion products

## Documentation for package ‘chimera’ version 1.22.0

- DESCRIPTION file.
- User guides, package vignettes and other documentation.
- Package NEWS.

## Help Pages

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