Standardise genes

Standardise gene symbols to HGNC.

standardise_genes(
  dat,
  gene_col = "gene_symbol",
  fill_na = TRUE,
  verbose = TRUE,
  ...
)

Arguments

dat

data.table

gene_col

character column name.

fill_na

logical. Fill NAs with original gene symbol.

verbose

logical. Print messages.

...

Arguments passed on to orthogene::map_genes

genes

Gene list.

species

Species to map against.

target

target namespace.

mthreshold

maximum number of results per initial alias to show. Shows all by default.

drop_na

Drop all genes without mappings. Sets gprofiler2::gconvert(filter_na=) as well an additional round of more comprehensive NA filtering by orthogene.

numeric_ns

namespace to use for fully numeric IDs (list of available namespaces).

run_map_species

Standardise species names with map_species first (Default: TRUE).

Value

data.table

Examples

if (FALSE) {
dat <- data.table(gene_symbol = c("BRCA1","BRCA2","BRCA3"))
dat2 <- standardise_genes(dat)
}