hgnc2pfam | R Documentation |
Mapping from Hugo symbol to Pfam-A domain composition.
If the given Hugo symbol has multiple UniProt ID mappings,
and guess == TRUE
,
the longest UniProt protein is selected. Return is either a list of a JSON.
hgnc2pfam(hgnc.symbol, guess = TRUE, uniprot.id = NA, output.format = "json")
hgnc.symbol |
primary Hugo symbol |
guess |
if the given Hugo symbol links to multiple UniProt IDs,
choose the longest one ( |
uniprot.id |
UniProt ID, in case that gene symbol maps to multiple UniProt entries. |
output.format |
output format: JSON or list |
A list or a JSON with attributes: symbol, uniprot, length, and a list of Pfam entries, including hmm.acc, hmm.name, start, end, and type.
# general usage hgnc2pfam("TP53") hgnc2pfam("TP53", output.format = "json") hgnc2pfam("TP53", output.format = "list") hgnc2pfam("TP53", output.format = "json", uniprot.id = "P04637") # OK # for gene mapping to multiple UniProt enties hgnc2pfam("GNAS", guess = TRUE) hgnc2pfam("GNAS", guess = FALSE) hgnc2pfam("GNAS", output.format = "list") hgnc2pfam("GNAS", output.format = "list", uniprot.id = "P84996") ## Not run: hgnc2pfam("GNAS", output.format = "list", uniprot.id = "P84997") # not exists, returns FALSE ## End(Not run) hgnc2pfam("PRAMEF9", output.format = "list") # no Pfam mappings
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