View source: R/resolve-gene-aliases.R
recode_alias | R Documentation |
Searches the Hugo Symbol column in a genomic dataframe to look for
any genes that have common gene name aliases,
and replaces those aliases with the accepted (most recent) gene name.
Function uses gnomeR::impact_alias_table
by default as reference for
which aliases to replace and supports IMPACT panel alias replacement only at this time.
Custom tables can be provided as long as hugo_symbol
and alias
columns exist.
recode_alias(genomic_df, alias_table = "impact", supress_warnings = FALSE)
genomic_df |
a gene_binary object |
alias_table |
a string indicating "impact" or "genie", or a dataframe with at least two columns ( |
supress_warnings |
If TRUE, function will return a list containing a dataframe of recoded results and a names vector of recoded aliases in data |
A dataframe with recoded Hugo Symbol columns
genomic_df <- rename_columns(gnomeR::mutations[1:5, ])
alias_table <- data.frame("hugo_symbol" = c("New Symbol", "New Symbol2"),
"alias" = c("PARP1", "AKT1"))
recode_alias(genomic_df, alias_table)
recode_alias(genomic_df, alias_table, supress_warnings = TRUE)
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