Read the output of KofamScan/KofamKoala or KAAS.

Source: R/2021_02_25-READ-read_ko.R

read_ko calculates the abundance of each KO within the bins based on the KofamScan or KofamKoala output.

read_ko(data_kofam=NULL, data_kaas=NULL, data_interpro=NULL)

Arguments

data_kofam

a path where KofamScan/KofamKoala output data are. They should have the extension .txt and it is recommended all files in the path are the ones that need to be read. Output data should have 5 columns with the bin names followed by the scaffold name divided by an “_”: bin_scaffoldXX.
data_kaas

a data frame with 2 columns. Contigs are expected to indicate in their names the bin name followed by the scaffold name divided by an "_": bin_scaffoldXX.
data_interpro

a data frame output of read_interpro. This argument is used within mapping_KO.

Details

This function is part of a package used for the analysis of bins metabolism.

Examples

if (FALSE) {
read_ko("C:/Users/bins")
}