CNA_gene: Extract per-gene copy number status.

In caravagnalab/CNAqc: CNAqc - Copy Number Analysis quality check

Extract per-gene copy number status.

Description

By default, this function maps a list of genes to their copy number status using clonal CNA segments. The genes used are all the known human genes, whose coordinates are available inside the CNAqc package and are identified by common names (e.g., TP53). The function can restrict to a subset of genes (faster computation) if one passes, via the 'genes' parameter, a vector of gene symbols.

Usage

CNA_gene(x, genes = NULL)

Arguments

x	A CNAqc object.
genes	Optional, a vector of gene symbols of interest. If 'NULL', all the human genes are used, according to the genome reference of input 'x'.

Value

A tibble with columns 'gene' (gene name), 'from'/'to' (gene delimiters), 'Major'/'minor'/'karyotype' as the information for the copy number segment where the gene sits. Note that if the gene maps to a subclonal segment this is not returned.

Examples

# Example input data released with the package
data('example_dataset_CNAqc', package = 'CNAqc')
print(example_dataset_CNAqc)

# Note the outputs to screen
x = init(mutations = example_dataset_CNAqc$mutations, cna = example_dataset_CNAqc$cna, purity = example_dataset_CNAqc$purity)

# Get mapping for all the known human genes - takes a bit longer
CNA_gene(x)

# Use known genes set
CNA_gene(x, genes = c("APC", "KRAS", "NRAS", "TP53"))

caravagnalab/CNAqc documentation built on Oct. 31, 2024, 3:54 a.m.