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Check signatures feasibility

Source: R/check_sig.R
check_sig.Rd

check_sig() is a helper function that shows useful information about signatures that you want to test on your gene expression matrix.

Usage

check_sig(expr_data, signatures = "all")

Arguments

expr_data

A normalized gene expression matrix (or data frame) with gene symbols as row names and samples as columns.

signatures

It can be a list of signatures or a character vector indicating keywords for a group of signatures. The default ("all") will cause the function to check for all the signatures implemented in hacksig.

Value

A tibble with a number of rows equal to the number of input signatures and five columns:

  • signature_id, a unique identifier associated to a signature;

  • n_genes, the number of genes composing a signature;

  • n_present and frac_present, the number and fraction of genes in a signature which are present in expr_data, respectively;

  • missing_genes, the missing gene symbols for each signature.

See also

get_sig_info(), hack_sig()

Examples

check_sig(test_expr)
#> # A tibble: 40 × 5
#>    signature_id              n_genes n_present frac_present missing_genes
#>    <chr>                       <int>     <int>        <dbl> <list>       
#>  1 wu2020_metabolic               30        20        0.667 <chr [10]>   
#>  2 muro2016_ifng                   6         4        0.667 <chr [2]>    
#>  3 liu2020_immune                  6         4        0.667 <chr [2]>    
#>  4 liu2021_mgs                     6         4        0.667 <chr [2]>    
#>  5 lu2020_npc                      3         2        0.667 <chr [1]>    
#>  6 estimate_stromal              141        91        0.645 <chr [50]>   
#>  7 she2020_irgs                   27        17        0.630 <chr [10]>   
#>  8 lohavanichbutr2013_hpvneg      13         8        0.615 <chr [5]>    
#>  9 eschrich2009_rsi               10         6        0.6   <chr [4]>    
#> 10 li2021_ferroptosis_a           10         6        0.6   <chr [4]>    
#> # … with 30 more rows
check_sig(test_expr, "estimate")
#> # A tibble: 2 × 5
#>   signature_id     n_genes n_present frac_present missing_genes
#>   <chr>              <int>     <int>        <dbl> <list>       
#> 1 estimate_stromal     141        91        0.645 <chr [50]>   
#> 2 estimate_immune      141        74        0.525 <chr [67]>