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

Value

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.

See also

gene_eval

Examples

data(iJO1366)
library(dplyr)
#> 
#> Attaching package: ‘dplyr’
#> The following objects are masked from ‘package:stats’:
#> 
#>     filter, lag
#> The following objects are masked from ‘package:base’:
#> 
#>     intersect, setdiff, setequal, union

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
)
#> # A tibble: 2,583 x 9
#>    abbreviation lowbnd uppbnd obj_coef equation officialName geneAssociation
#>    <chr>         <dbl>  <dbl>    <dbl> <chr>    <chr>        <chr>          
#>  1 12DGR120tipp      0   1000        0 12dgr12… 1,2 diacylg… ""             
#>  2 12DGR140tipp      0   1000        0 12dgr14… 1,2 diacylg… ""             
#>  3 12DGR141tipp      0   1000        0 12dgr14… 1,2 diacylg… ""             
#>  4 12DGR160tipp      0   1000        0 12dgr16… 1,2 diacylg… ""             
#>  5 12DGR161tipp      0   1000        0 12dgr16… 1,2 diacylg… ""             
#>  6 12DGR180tipp      0   1000        0 12dgr18… 1,2 diacylg… ""             
#>  7 12DGR181tipp      0   1000        0 12dgr18… 1,2 diacylg… ""             
#>  8 12PPDRtex     -1000   1000        0 12ppd__… (R)-Propane… "b0241 | b0929…
#>  9 12PPDRtpp     -1000   1000        0 12ppd__… (R)-Propane… ""             
#> 10 12PPDStex     -1000   1000        0 12ppd__… (S)-Propane… "b0241 | b0929…
#> # … with 2,573 more rows, and 2 more variables: subsystem <chr>, present <dbl>