Read the output of KofamScan/KofamKoala or KAAS.

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

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

Arguments

data_kofam

a file output of KofamScan/KofamKoala. 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.

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 a '-' or '_': 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) { # \dontrun{
read_ko_shiny("Kofam_output")
} # }