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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 |