Calculate per group copy number for a list of genes.
Usage
get_gene_copy(
sce,
assay_name,
group_var = "all",
gain_cutoff = 0.75,
loss_cutoff = -gain_cutoff,
clonal_thr = 0.75,
gene_names = NULL,
cancer_genes = TRUE
)Arguments
- sce
Single cell experiment object
- assay_name
Name of the assay from which to pull copy number
- group_var
Grouping variable (defaults to all)
- gain_cutoff
Relative copy increase to be considered a copy gain
- loss_cutoff
Relative copy decrease to be considered a copy loss
- clonal_thr
Proportion of clones harboring a gain or loss to be considered clonal
- gene_names
List of genes to get copy number
- cancer_genes
Logical. Whether to include results for cancer genes. Default=TRUE.
Value
A list with three elements:
- copy
Wide form data frame with one row per gene, and columns reflecting the average per clone copy, the relative copy increase or decrease versus clone average copy, clone average copy
- copy_long
A melted version of
copy- clonal
A filtered version of
copy_longthat classifies each mutation as private, shared, or clonal, and whether the type of gain or loss matches the gene's oncogene or tumor suppressor type.