Create design matrix. — create_model

Store term membership for each gene.

create_model_df(df_genes, df_terms, pvalue_threshold = 0.05)

Arguments

df_genes: Dataframe storing gene names and DE p-values.
df_terms: Dataframe storing pathway database.
pvalue_threshold: P-value threshold to create binary columns `pvalue_sig` and `pvalue_notsig`.

Value

Dataframe.

Examples

df_genes <- data.frame(
  gene = c("g1", "g2"),
  pvalue = c(0.1, 0.2)
)
df_terms <- data.frame(
  term = c("A", "A", "B", "B", "C"),
  gene = c("g1", "g2", "g1", "g2", "g2")
)
create_model_df(df_genes, df_terms)
#> # A tibble: 2 × 7
#>   gene  pvalue A.member B.member C.member pvalue_sig pvalue_notsig
#>   <fct>  <dbl> <lgl>    <lgl>    <lgl>    <lgl>      <lgl>        
#> 1 g1       0.1 TRUE     TRUE     FALSE    FALSE      TRUE         
#> 2 g2       0.2 TRUE     TRUE     TRUE     FALSE      TRUE