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,
write=FALSE)a path where KofamScan/KofamKoala output data are. They should have the extension .txt and 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 a '-' or '_': bin_scaffoldXX.
a data frame with 2 columns. Contigs are expected to indicate in their names the bin name followed by the scaffold name divided by a '-' or '_': bin_scaffoldXX.
a data frame output of read_interpro. This argument is used within mapping_ko.
a logical value indicating to save the data imported as a formatted table with .tsv extension with a time stamp and it will be located in your current working directory
This function is part of a package used for the analysis of bins metabolism.
read_ko ("C:/Users/bins/", write = FALSE)
#> Error in map(.x, .f, ...): ℹ In index: 1.
#> Caused by error:
#> ! 'C:/Users/bins/' does not exist.