hgnc2pfam: Map from Hugo symbol to Pfam domains

In g3viz: Interactively Visualize Genetic Mutation Data using a Lollipop-Diagram

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")

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

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.

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")
## Not run: 
hgnc2pfam("GNAS", output.format = "list", uniprot.id = "P84997") # , returns FALSE

## End(Not run)

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

g3viz documentation built on Sept. 11, 2024, 9:25 p.m.