Description Usage Arguments Value Warning See Also Examples
View source: R/gene_associate.R
A convenience function that uses gene_eval
and a custom function to apply new upper and lower bounds.
1 2 3 4 5 6 | gene_associate(
reaction_table,
gene_table,
expression_flux_function = function(x) { (1 + log(x)/stats::sd(x)^2)^sign(x - 1)
}
)
|
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 |
the reaction_table, with a new column, present, and altered upper and lower bounds
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.
gene_eval
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 | 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
)
|
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