likely_symbol {convertid}

Retrieve Symbol Aliases and Previous symbols to determine a likely current symbol

Description

likely_symbol() downloads the latest version of the HGNC gene symbol database as a text file and query it to obtain symbol aliases, previous symbols and all symbols currently in use. (Optionally) assuming the input ID to be either an Alias or a Symbol or a Previous Symbol it performs multiple queries and compares the results of all possible combinations to determine a likely current Symbol.

Usage

likely_symbol(
  syms,
  alias_sym = TRUE,
  prev_sym = TRUE,
  orgnsm = "human",
  hgnc = NULL,
  hgnc_url = NULL,
  output = c("likely", "symbols", "all"),
  verbose = TRUE
)

Arguments

syms

(character). Vector of Gene Symbols to be tested.

alias_sym

(logical). Should the input be assumed to be an Alias? Defaults to TRUE.

prev_sym

(logical). Should the input be assumed to be a Previous Symbol? Defaults to TRUE.

orgnsm

(character). The organism for which the Symbols are tested.

hgnc

(data.frame). An optional data frame with the needed HGNC annotations. (Needs to match the format available at hgnc_utl!)

hgnc_url

(character). URL where to download the HGNC annotation dataset. Defaults to "ftp://ftp.ebi.ac.uk/pub/databases/genenames/new/tsv/hgnc_complete_set.txt".

output

(character). One of "likely", "symbols" and "all". Determines the scope of the output data frame. Defaults to "likely" which will return the inout Symbol and the determined likely Symbol.

verbose

(logical). Should messages be written to the console? Defaults to TRUE.

Details

Please note that the algorithm is very slow for large input vectors.

Value

A data.frame with the following columns depending on the output setting. output="likely":

	'likely_symbol'
	'input_symbol'

output="symbols":

	'current_symbols'
	'likely_symbol'
	'input_symbol'
	'all_symbols'

output="all":

	'orig_input'
	'organism'
	'current_symbols'
	'likely_symbol'
	'input_symbol'
	'all_symbols'

Note

Only fully implemented for Human for now.

Examples

## Not run: 
likely_symbol(c("ABCC4", "ACPP", "KIAA1524"))

## End(Not run)