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Summarise a Genotype Table

Source: R/summarise.R
summarise_geno.Rd

summarise_geno() computes summary information for a genotype table.

Usage

summarise_geno(
  geno_table,
  sample_col = "id",
  marker_col = "marker",
  drug_col = "drug",
  class_col = "drug_class",
  gene_col = "gene",
  variation_col = "variation type",
  force_ab = FALSE
)

Arguments

geno_table

A tibble or data frame containing genotype data, in the format output by import_amrfp.

sample_col

Character. Name of the column containing sample identifiers. Default is "id".

marker_col

Character. Name of the column containing marker identifiers. Default is "marker".

drug_col

Character. Name of the column containing drug agent identifiers. Default is "drug". If this is of class 'ab' the entries will be annotated with their full antibiotic names, converted using AMR::as.ab. If this is desired behaviour but the class is not 'ab', set force_ab=TRUE.

class_col

Character. Name of the column containing drug class identifiers. Default is "drug_class".

gene_col

Character. Name of the column containing gene identifiers. Default is "gene".

variation_col

Character. Name of the column containing variation type identifiers. Default is "variation type".

force_ab

Logical. If TRUE, attempts to convert entries in drug_col to antibiotic names using AMR::as.ab even if this column is not of class "ab" Default is FALSE.

Value

A named list with the following elements:

  • uniques: A tibble of the number of unique samples, markers, genes, drugs, classes and variation types detected in geno_table.

  • per_type: A tibble of unique counts of samples, markers, genes, drugs, and classes per variation type.

  • drugs: A tibble listing the drugs and/or drug classes represented in the table, and the associated number of unique markers, unique samples, and total hits for each drug/class.

  • markers: A tibble listing the markers represented in the table, and the associated drugs/classes and variation types (if present). Number indicates the count of hits detected per marker.

Details

The function automatically adapts to the presence or absence of columns in geno_table. The force_ab parameter allows the addition of full antibiotic names using the ab_name() function even when the first column is not recognized as an "ab" object.

Examples


summarise_geno(staph_geno_ebi)
#> $uniques
#> # A tibble: 5 × 2
#>   column     n_unique
#>   <chr>         <int>
#> 1 id             7547
#> 2 marker           22
#> 3 drug             13
#> 4 drug_class        6
#> 5 gene             22
#> 
#> $per_type
#> NULL
#> 
#> $drugs
#> # A tibble: 15 × 6
#>    drug drug_name     drug_class      markers samples  hits
#>    <ab> <chr>         <chr>             <int>   <int> <int>
#>  1 AMK  Amikacin      Aminoglycosides       6    1941  7745
#>  2 APR  Apramycin     Aminoglycosides       1      12    12
#>  3 CLI  Clindamycin   Lincosamides          1       1     8
#>  4 DOX  Doxycycline   Tetracyclines         1       1     8
#>  5 ERY  Erythromycin  Macrolides            1       1     8
#>  6 GEN  Gentamicin    Aminoglycosides       5     981  4321
#>  7 KAN  Kanamycin     Aminoglycosides       6    1963  7861
#>  8 MNO  Minocycline   Tetracyclines         1       1     8
#>  9 SPT  Spectinomycin Other                 2    1475  1671
#> 10 STR1 Streptomycin  Aminoglycosides       3     497   582
#> 11 TGC  Tigecycline   Tetracyclines         2    7538  7576
#> 12 TOB  Tobramycin    Aminoglycosides       5    1004  4445
#> 13 NA   NA            Aminoglycosides       2      43    43
#> 14 NA   NA            Pleuromutilins        1       1     8
#> 15 NA   NA            Tetracyclines         6    7525 11649
#> 
#> $markers
#> # A tibble: 43 × 5
#>    marker                 drug drug_name     drug_class          n
#>    <chr>                  <ab> <chr>         <chr>           <int>
#>  1 aac(6')-Ie             AMK  Amikacin      Aminoglycosides     9
#>  2 aac(6')-Ie             KAN  Kanamycin     Aminoglycosides     9
#>  3 aac(6')-Ie             TOB  Tobramycin    Aminoglycosides     9
#>  4 aac(6')-Ie/aph(2'')-Ia AMK  Amikacin      Aminoglycosides  4272
#>  5 aac(6')-Ie/aph(2'')-Ia GEN  Gentamicin    Aminoglycosides  4272
#>  6 aac(6')-Ie/aph(2'')-Ia KAN  Kanamycin     Aminoglycosides  4272
#>  7 aac(6')-Ie/aph(2'')-Ia TOB  Tobramycin    Aminoglycosides  4272
#>  8 aadD1                  KAN  Kanamycin     Aminoglycosides   124
#>  9 aadD1                  TOB  Tobramycin    Aminoglycosides   124
#> 10 ant(3'')-IIa           SPT  Spectinomycin Other               2
#> # ℹ 33 more rows
#>