import_aeron: Import results from an Aeron run into a list of Fusion...

Description Usage Arguments Details Value Examples

View source: R/import_aeron.R

Description

A function that imports the results from an Aeron run into a list of Fusion objects.

Usage

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import_aeron(
  filename_fusion_support,
  filename_fusion_transcript,
  genome_version,
  limit
)

Arguments

filename_fusion_support

Filename for the Aeron result file fusion_support..txt.

filename_fusion_transcript

Filename for the Aeron result file fusion_transcripts..txt.

genome_version

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

limit

A limit on how many lines to read.

Details

Note that the strands and breakpoint positions are not included in the result files from Aeron. These have to be retrieved manually, using the ensembl identifiers (which are included in the result files, and will be available in the Fusion objects after importing).

Value

A list of Fusion objects.

Examples

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aeronfusionsupportfile <- system.file(
  "extdata",
  "aeron_fusion_support.txt",
  package="chimeraviz")
aeronfusiontranscriptfile <- system.file(
  "extdata",
  "aeron_fusion_transcripts.fa",
  package="chimeraviz")
fusions <- import_aeron(
  aeronfusionsupportfile,
  aeronfusiontranscriptfile,
  "hg19",
  3)
# This should import a list of 3 fusions described in Fusion objects.

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