This function lets you add a fusion read alignment file to a fusion object. If you've mapped the reads supporting a fusion against the fusion junction sequence, and have the resulting bamfile, use this function to add the information (as a Gviz::GAlignmentPairs object) to the fusion object.
The fusion object to add a genomic alignment to.
The bam file containing the fusion reads plotted to the fusion sequence.
An updated fusion object with fusion@fusion_reads_alignment set.
# Load data defuse833ke <- system.file( "extdata", "defuse_833ke_results.filtered.tsv", package="chimeraviz") fusions <- import_defuse(defuse833ke, "hg19", 1) # Find the specific fusion we have aligned reads for fusion <- get_fusion_by_id(fusions, 5267) # Get reference to the bamfile with the alignment data bamfile5267 <- system.file( "extdata", "5267readsAligned.bam", package="chimeraviz") # Add the bam file of aligned fusion reads to the fusion object fusion <- add_fusion_reads_alignment(fusion, bamfile5267)
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