Description Usage Arguments Value Examples
Functions for creating BiocSet
objects from GO sets and
KEGG sets, and creating a new set mapping from a current BiocSet
object. map_add_set
will add the mapping as a new column instead
of overwriting the current one used for the mapping.
1 2 3 4 5 6 7 |
org |
The AnnotationDbi object to identify keys/mappings from. |
from |
A character to indicate which identifier to map from. |
go |
A character to indicate the column name for the GO ids. Default is "GO". |
evidence |
A character to indicate the evidence codes for GO associations with a gene of interest. Default is all possible evidence codes. |
ontology |
A character to indicate which Gene Ontology to use. Default is BP, CC, and MF. |
species |
Which species the pathways are from. |
.data |
The BiocSet object that contains the set tibble being mapped. |
to |
A character to indicate which identifier to map to. |
add |
The id to add to the |
For go_sets
, a BiocSet
object with GO ids as the set
ids.
For kegg_sets
, a BiocSet
object with Entrez IDs
reported as elements (default from KEGGREST) and KEGG pathways as sets.
For map_set
, a BiocSet object with the mapped set present in
the set tibble.
For map_add_set
, a BiocSet
object with a new column in
the set tibble with the mapping of the new id type.
1 2 3 4 5 6 7 8 9 10 11 | library(org.Hs.eg.db)
go <- go_sets(org.Hs.eg.db, "ENSEMBL")
kegg_sets("hsa")
es <- BiocSet(set1 = letters, set2 = LETTERS)
es %>% map_set("set1", "foo")
library(GO.db)
map <- map_add_set(go, GO.db, "GOID", "DEFINITION")
go %>% mutate_set(definition = map)
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