gene_associate function

Apply gene expressions to reaction table

Apply gene expressions to reaction table

A convenience function that uses gene_eval and a custom function to apply new upper and lower bounds.

gene_associate( reaction_table, gene_table, expression_flux_function = function(x) { (1 + log(x)/stats::sd(x)^2)^sign(x - 1) } )

Arguments

  • reaction_table: A data frame describing the metabolic model.
  • gene_table: A data frame showing gene presence
  • expression_flux_function: a function to convert from gene set expression to flux

Returns

the reaction_table, with a new column, present, and altered upper and lower bounds

Warning

This function relies on gene_eval, which uses eval to evaluate gene expression sets. This gives flexibility, but means that malicious code in the gene_sets argument could get evaluated. gene_sets is evaluated in a restricted environment, but there might be a way around this, so you might want to check for anything suspicious in this argument manually. For more information, read the code.

Examples

data(iJO1366) library(dplyr) gene_table = tibble(name = iJO1366$geneAssociation %>% stringr::str_split('and|or|\\s|\\(|\\)') %>% purrr::flatten_chr() %>% unique, presence = 1) %>% filter(name != '', !is.na(name)) gene_associate(reaction_table = iJO1366 %>% mutate(geneAssociation = geneAssociation %>% stringr::str_replace_all('and', '&') %>% stringr::str_replace_all('or', '|') ), gene_table = gene_table )

See Also

gene_eval