import_soapfuse: Import results from a SOAPfuse run into a list of Fusion...

Description Usage Arguments Value Examples

Description

A function that imports the results from a SOAPfuse run, typically from a final.Fusion.specific.for.genes file, into a list of Fusion objects.

Usage

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import_soapfuse(filename, genome_version, limit)

Arguments

filename

Filename for the SOAPfuse final-list-candidate-fusion-genes.txt results file.

genome_version

Which genome was used in mapping (hg19, hg38, etc.).

limit

A limit on how many lines to read.

Value

A list of Fusion objects.

Examples

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soapfuse833ke <- system.file(
  "extdata",
  "soapfuse_833ke_final.Fusion.specific.for.genes",
  package = "chimeraviz")
fusions <- import_soapfuse(soapfuse833ke, "hg19", 3)
# This should import a list of 3 fusions described in Fusion objects.

chimeraviz documentation built on Jan. 19, 2021, 2 a.m.