summarise_pheno() computes summary information for a phenotype table.
Usage
summarise_pheno(
pheno_table,
sample_col = "id",
drug_col = "drug_agent",
mic_col = "mic",
disk_col = "disk",
spp_col = "spp_pheno",
pheno_cols = NULL,
method_cols = c("method", "platform", "guideline", "source"),
force_ab = FALSE
)Arguments
- pheno_table
A tibble or data frame containing phenotype data, in the format output by import_ast.
- sample_col
Character. Name of the column containing sample identifiers. Default is
"id".- 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', setforce_ab=TRUE.- mic_col
Character. Name of the column containing MIC data. Default is
"mic".- disk_col
Character. Name of the column containing drug class identifiers. Default is
"disk".- spp_col
Character. Name of the column containing species names Default is
"spp_pheno".- pheno_cols
Vector. Vector giving names of columns containing categorical phenotype calls (S/I/R or NWT/WT). Default is any columns beginning with
"pheno"or"ecoff".- method_cols
Vector. Vector giving names of columns containing method or source information by which to summarise MIC/disk data. Default is
c("method", "platform", "guideline", "source").- force_ab
Logical. If
TRUE, attempts to convert entries indrug_colto antibiotic names using AMR::as.ab even if this column is not of class"ab"Default isFALSE.
Value
A named list with the following elements:
- uniques
A tibble of the number of unique samples, drugs, organisms, and methods detected in
pheno_table.- drugs
A tibble listing the drugs included in the table, and the associated number of samples with MIC measures, disk measures, neither or both, for each drug and species.
- details
A tibble listing more details of the methods of assay measurements, per drug and species.
- pheno_counts_list
A list of tibbles, each corresponding to a unique categorical phenotype column in the input, indicating the counts of each phenotypic category per drug and species.
Details
The function automatically adapts to the presence or absence of columns in pheno_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_pheno(staph_ast_ebi)
#> No phenotype column names provided via 'pheno_cols'
#> These are needed to summarise counts of phenotype category calls per drug.
#> Relevant columns detected in your input table are: c('pheno_provided','pheno_eucast','pheno_clsi','pheno_eucast_mic','pheno_eucast_disk','pheno_clsi_mic','pheno_clsi_disk','ecoff','ecoff_mic','ecoff_disk')
#> $uniques
#> # A tibble: 7 × 2
#> column n_unique
#> <chr> <int>
#> 1 id 190
#> 2 drug_agent 2
#> 3 spp_pheno 1
#> 4 method 3
#> 5 platform 2
#> 6 guideline 2
#> 7 source 2
#>
#> $drugs
#> # A tibble: 2 × 6
#> drug_agent antibiotic_name spp_pheno disk mic none
#> <ab> <chr> <chr> <int> <int> <int>
#> 1 AMK Amikacin Staphylococcus aureus 3 11 70
#> 2 DOX Doxycycline Staphylococcus aureus NA 47 87
#>
#> $details
#> # A tibble: 6 × 10
#> drug_agent antibiotic_name spp_pheno method platform guideline source mic
#> <ab> <chr> <chr> <chr> <chr> <chr> <chr> <int>
#> 1 AMK Amikacin Staphylococ… broth… Vitek CLSI NA 1
#> 2 AMK Amikacin Staphylococ… disk … NA CLSI NA NA
#> 3 AMK Amikacin Staphylococ… disk … NA NA 27150… NA
#> 4 AMK Amikacin Staphylococ… NA NA NA NA 10
#> 5 DOX Doxycycline Staphylococ… broth… NA CLSI NA 29
#> 6 DOX Doxycycline Staphylococ… NA NA NA NA 18
#> # ℹ 2 more variables: disk <int>, none <int>
#>
#> $pheno_counts_list
#> list()
#>
summarise_pheno(staph_ast_ebi, pheno_cols = c("pheno_provided", "pheno_clsi", "ecoff"))
#> $uniques
#> # A tibble: 7 × 2
#> column n_unique
#> <chr> <int>
#> 1 id 190
#> 2 drug_agent 2
#> 3 spp_pheno 1
#> 4 method 3
#> 5 platform 2
#> 6 guideline 2
#> 7 source 2
#>
#> $drugs
#> # A tibble: 2 × 6
#> drug_agent antibiotic_name spp_pheno disk mic none
#> <ab> <chr> <chr> <int> <int> <int>
#> 1 AMK Amikacin Staphylococcus aureus 3 11 70
#> 2 DOX Doxycycline Staphylococcus aureus NA 47 87
#>
#> $details
#> # A tibble: 6 × 10
#> drug_agent antibiotic_name spp_pheno method platform guideline source mic
#> <ab> <chr> <chr> <chr> <chr> <chr> <chr> <int>
#> 1 AMK Amikacin Staphylococ… broth… Vitek CLSI NA 1
#> 2 AMK Amikacin Staphylococ… disk … NA CLSI NA NA
#> 3 AMK Amikacin Staphylococ… disk … NA NA 27150… NA
#> 4 AMK Amikacin Staphylococ… NA NA NA NA 10
#> 5 DOX Doxycycline Staphylococ… broth… NA CLSI NA 29
#> 6 DOX Doxycycline Staphylococ… NA NA NA NA 18
#> # ℹ 2 more variables: disk <int>, none <int>
#>
#> $pheno_counts_list
#> $pheno_counts_list$pheno_provided
#> # A tibble: 2 × 6
#> drug_agent antibiotic_name spp_pheno S R I
#> <ab> <chr> <chr> <int> <int> <int>
#> 1 AMK Amikacin Staphylococcus aureus 12 72 NA
#> 2 DOX Doxycycline Staphylococcus aureus 103 20 11
#>
#> $pheno_counts_list$pheno_clsi
#> # A tibble: 2 × 7
#> drug_agent antibiotic_name spp_pheno `NA` S I R
#> <ab> <chr> <chr> <int> <int> <int> <int>
#> 1 AMK Amikacin Staphylococcus aureus 84 NA NA NA
#> 2 DOX Doxycycline Staphylococcus aureus 87 41 5 1
#>
#> $pheno_counts_list$ecoff
#> # A tibble: 2 × 7
#> drug_agent antibiotic_name spp_pheno WT NWT `NA` NI
#> <ab> <chr> <chr> <int> <int> <int> <int>
#> 1 AMK Amikacin Staphylococcus aureus 12 2 70 NA
#> 2 DOX Doxycycline Staphylococcus aureus NA 9 87 38
#>
#>