add_fusion_reads_alignment {chimeraviz} | R Documentation

## Add fusion reads alignment to fusion object

### Description

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.

### Usage

    add_fusion_reads_alignment(fusion, bamfile)

### Arguments

`fusion` | The fusion object to add a genomic alignment to.
`bamfile` | The bam file containing the fusion reads plotted to the fusion sequence.

### Value

An updated fusion object with fusion@fusion_reads_alignment set.

### Examples

    # 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)

[Package chimeraviz version 1.13.8 Index]