read_dbcan3: Read the output of dbCAN and extract abundance profile

In mirnavazquez/RbiMs: R Tools for Reconstruncting Bin Metabolisms

Read the output of dbCAN and extract abundance profile

Description

read_dbcan3 calculates the abundance of each Gene within the bins based on the dbCAN output from run_dbcan3 V3.0.6.

Usage

read_dbcan3(dbcan_path, write=FALSE, profile=TRUE)

Arguments

dbcan_path	a path where dbCAN output data are. They should have the extension overview.txt and all files in the path are the ones that need to be read. Output data should have 6 columns with the bin names followed by the Genes obtained in every algorithm (HMMER,Hotpep,DIAMOND), column 'Signalp' indcating if a Peptide signal is found and a column '#ofTools" indicating the number of algorithms that found this Gene.
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 workin directory
profile	a logical value indicating if you want to print a profile or not.

Examples

## Not run: 
read_dbcan3("C:/Users/bins/")

## End(Not run)

mirnavazquez/RbiMs documentation built on Sept. 6, 2024, 1:05 p.m.