read_ko: Read the output of KofamScan/KofamKoala or KAAS.

In mirnavazquez/RbiMs: R Tools for Reconstruncting Bin Metabolisms

Read the output of KofamScan/KofamKoala or KAAS.

Description

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

Usage

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

Arguments

data_kofam	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.
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.
write	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

Details

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

Examples

## Not run: 
read_ko("C:/Users/bins/", write=FALSE)

## End(Not run)

mirnavazquez/RbiMs documentation built on March 6, 2024, 10:27 p.m.