Search for matches to antibody names in gene aliases data set

Search gene symbols, aliases and names for an exact match to an value, assumed to be an antigen name or part of an antigen name. query_df must have columns named "ID", "name" and "value". "name" is used for checking whether the value is formatted as a multi-subunit protein.

Usage

searchAliases(query_df, multisubunit = c("TCR_long", "subunit"))

Arguments

query_df

A data.frame in long format for searching for exact matches to HGNC names. Must contain a column "value" containing potential gene symbols for matching with HGNC symbols and descriptions, a column "ID" for grouping results, and a column "name" indicating the type of match (only used for multi-subunit proteins and TCRs).

multisubunit

character(n) Name(s) of entries in "name" column corresponding to multi-subunit proteins. Use NA if none exist.

Value

A data.frame of matches from IDs in query_df to HGNC genes, including a column "n_matches" giving the number of matches to different genes.