g3viz (version 1.2.0)

hgnc2pfam: Map from Hugo symbol to Pfam domains

Description

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.

Usage

hgnc2pfam(hgnc.symbol, guess = TRUE, uniprot.id = NA, output.format = "json")

Value

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.

Arguments

hgnc.symbol

primary Hugo symbol

guess

if the given Hugo symbol links to multiple UniProt IDs, choose the longest one (guess == TRUE); otherwise NA (guess == FALSE). Default TRUE.

uniprot.id

UniProt ID, in case that gene symbol maps to multiple UniProt entries.

output.format

output format: JSON or list

Examples

# 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")
if (FALSE) {
hgnc2pfam("GNAS", output.format = "list", uniprot.id = "P84997") # , returns FALSE
}

hgnc2pfam("PRAMEF9", output.format = "list") # no Pfam mappings