classifyAllMDRfromRSI: Classify the multi-drug resistance for multiple samples

In Cloris2000/MDRClassifier: Multi-Drug Resistance Classifier

Description

A function that classify the multi-drug resistances of all samples in the csv file given the all drug resistances information from RGI prediction. The number of antimicrobial agents tested determines which version of the multi-drug resistance category to use. If all antimicrobial agents are tested and given,then use the criteria given by ECDC. Otherwise, we use more specific criteria by subdividing ECDC criteria to generate reasonable MDR categories.

Usage

classifyAllMDRfromRSI(RSI_table, total_cat)

Arguments

RSI_table	A list with each row representing each sample IDs and one of the columns is the string of drugs that the sample resistant.
total_cat	The integer number of total antimicrobial category of species. mode is set to "complete" by default. If all antimicrobial agents are tested and given,then use "complete" mode. Otherwise, use "partial" mode to generate reasonable MDR categories.

Value

Returns a dataframe with each row name representing the sample ID and its column representing the MDR category.

Examples

# Example 6
# Using RSI_table dataset available with package
#classify the category of all samples' multi-drug resistance
resultsExample6 <- classifyAllMDRfromRSI(RSI_table = RSI_table, total_cat = 8)
# To obtain value from results
resultsExample6

Cloris2000/MDRClassifier documentation built on Dec. 17, 2021, 2:06 p.m.