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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 = "Name",
  marker_col = "marker",
  drug_col = "drug_agent",
  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 "Name".

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_agent". 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


geno_table <- import_amrfp(ecoli_geno_raw)
summarise_geno(geno_table)
#> $uniques
#> # A tibble: 6 × 2
#>   column         n_unique
#>   <chr>             <int>
#> 1 Name               5258
#> 2 marker              244
#> 3 drug_agent           35
#> 4 drug_class           26
#> 5 gene                196
#> 6 variation type        5
#> 
#> $per_type
#> # A tibble: 5 × 6
#>   `variation type`                Name marker drug_agent drug_class  gene
#>   <chr>                          <int>  <int>      <int>      <int> <int>
#> 1 Gene presence detected          5258    164         22         17   164
#> 2 Inactivating mutation detected   615     42         15         14    42
#> 3 Nucleotide variant detected       57      2          3          3     1
#> 4 Promoter variant detected         93      4          1          1     1
#> 5 Protein variant detected        4920     65         18         16    21
#> 
#> $drugs
#> # A tibble: 44 × 6
#>    drug_agent antibiotic                  drug_class       markers samples  hits
#>    <ab>       <chr>                       <chr>              <int>   <int> <int>
#>  1 AMC        Amoxicillin/clavulanic acid Aminopenicillins       2      57    57
#>  2 AMK        Amikacin                    Aminoglycosides        6     176   180
#>  3 AMP        Ampicillin                  Aminopenicillins       6     749   749
#>  4 APR        Apramycin                   Aminoglycosides        1      98    98
#>  5 ATM        Aztreonam                   Monobactams            2      39    39
#>  6 AZM        Azithromycin                Macrolides             4     472   478
#>  7 BLM        Bleomycin                   Glycopeptides          2      40    40
#>  8 CHL        Chloramphenicol             Phenicols             15    1121  1181
#>  9 CLI        Clindamycin                 Lincosamides           1      26    26
#> 10 CLR        Clarithromycin              Macrolides             1       1     1
#> # ℹ 34 more rows
#> 
#> $markers
#> # A tibble: 349 × 6
#>    marker      drug_agent antibiotic  drug_class      `variation type`         n
#>    <chr>       <ab>       <chr>       <chr>           <chr>                <int>
#>  1 aac(2')-IIa KAS        Kasugamycin Aminoglycosides Gene presence detec…     1
#>  2 aac(3)-II   GEN        Gentamicin  Aminoglycosides Inactivating mutati…     1
#>  3 aac(3)-IId  GEN        Gentamicin  Aminoglycosides Gene presence detec…   204
#>  4 aac(3)-IId  GEN        Gentamicin  Aminoglycosides Inactivating mutati…     1
#>  5 aac(3)-IIe  GEN        Gentamicin  Aminoglycosides Gene presence detec…   120
#>  6 aac(3)-IIg  GEN        Gentamicin  Aminoglycosides Gene presence detec…     2
#>  7 aac(3)-IVa  APR        Apramycin   Aminoglycosides Gene presence detec…    98
#>  8 aac(3)-IVa  GEN        Gentamicin  Aminoglycosides Gene presence detec…    98
#>  9 aac(3)-IVa  TOB        Tobramycin  Aminoglycosides Gene presence detec…    98
#> 10 aac(3)-Ib   GEN        Gentamicin  Aminoglycosides Gene presence detec…     1
#> # ℹ 339 more rows
#>