Description Usage Arguments Value Examples
map_genes
provides mapping to ENTREZ gene identifiers for Hugo or
Ensembl gene identifiers using either org.Mm.eg.db or org.Hs.eg.db Bioconductor annotation
packages. Function annotate::lookUp()
extract the mappings. We use ALIAS2EG
for Hugo - ENTREZ
mappings and ENSEMBL
for Ensembl - ENTREZ gene mappings.
1 | map_genes(dat, id, species)
|
dat |
Data frame with two columns: id and set_label. |
id |
A character string specifying the type of gene identifier in the data, must of be one of two "symbol" (default) or "ensembl". |
species |
A character string specifying the species, must be one of two "human" (default) or "mouse". |
Data frame with two columns: entrez and set_label. The column with the original identifiers is removed.
1 2 3 4 5 6 7 8 9 | ## Not run:
# load test data:
data("human_symbol")
# remove duplicate rows:
dat_clean <- deduplicate_rows(human_symbol)
# map symbol to ENTREZ gene id:
dat_mapped <- map_genes(dat_clean, id = "symbol", species = "human")
## End(Not run)
|
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