find fusions

annotates all gene fusions in gGraph relative to cds definitions

cds = gencode cds GRanges gff3 / gtf or GRangesList the latter (converted via rtracklayer::import) which has fields $exon_number

"gene_name" GRangesList meta data field is used in annotation and in not creating "splice" fusionsthat arise from different transcripts of the same gene.

fusions(
  graph = NULL,
  gencode = NULL,
  genes = NULL,
  annotate.graph = TRUE,
  mc.cores = 1,
  verbose = FALSE
)

Arguments

graph

input gGraph

gencode

GFF containing gene boundaries and exons, in similar format to https://www.gencodegenes.org/

genes

set of genes to pass for fusions.

annotate.graph

Annotate the graph generated Default: True

mc.cores

number of cores to run. Default: 1

verbose

output verbose argument to function Default: False

Value

gWalks of gene fusions annotated with frame and gene(s)

Details

For more info please follow the protein fusions analysis in the gGnome Tutorial:

Protein fusions