get_gene_copy_numbers: get_gene_copy_numbers

In mskilab/casereport: casereport: Whole-genome + transcription based report for cancer genomes

get_gene_copy_numbers

Description

Takes a jabba_rds output and returns a GRanges with the genes that have either amplifications or deletions

Usage

get_gene_copy_numbers(
  gg,
  gene_ranges,
  complex.fname = NULL,
  nseg = NULL,
  gene_id_col = "gene_id",
  simplify_seqnames = FALSE,
  mfields = c("gene_name", "source", "gene_id", "gene_type", "level", "hgnc_id",
    "havana_gene"),
  ev.types = c("qrp", "qpdup", "qrdel", "tic", "bfb", "dm", "chromoplexy",
    "chromothripsis", "tyfonas", "rigma", "pyrgo", "cpxdm"),
  output_type = "data.table",
  ploidy = 2,
  verbose = TRUE
)

Arguments

gg	either path to rds of a gGraph or an object containing the gGraph with JaBbA output
gene_ranges	GRanges of genes (must contain field "gene_name"). Alternatively a path to a file that could be parsed by rtracklayer::import (such as gtf) is acceptable.
complex.fname	(character) path to complex event calls
nseg	GRanges with field "ncn" - the normal copy number (if not provided then ncn = 2 is used)
gene_id_col	the name of the column to be used in order to identify genes (must be unique for each gene, so usually "gene_name" is not the right choice).
simplify_seqnames	when set to TRUE, then gr.sub is ran on the seqnames of the gGraph segments and the genes GRanges
mfields	the metadata fields that the output should inherit from the genes GRanges
ev.types	complex event types (for now excluding simple dups/dels...)
output_type	either GRanges or data.table
ploidy	tumor ploidy default 2

Value

GRanges or data.table with genes CN

Author(s)

Alon Shaiber

mskilab/casereport documentation built on Oct. 19, 2022, 3 a.m.