read_interpro: Extract abundance profile of InterProScan output.

In mirnavazquez/RbiMs: R Tools for Reconstruncting Bin Metabolisms

Extract abundance profile of InterProScan output.

Description

Reads a table object created with InterProScan and generates a profile table of abundance with the hits of the KEGG, PFAM or INTERPRO databases. The output of KEGG database can be used within mapping_ko.

Usage

read_interpro(data_interpro, 
database=c("KEGG", "Pfam", "INTERPRO",
"TIGRFAM", "SUPERFAMILY", "SMART", "SFLD", "ProSiteProfiles",
"ProSitePatterns", "ProDom", "PRINTS", "PIRSF", 
"MobiDBLite","Hamap", "Gene3D", "Coils", "CDD"), profile = TRUE)

Arguments

data_interpro	a table, output of InterProScan on tsv format. InterProScan should have been run with -pa option to be able to use the KEGG option, in the database argument.
database	a character indicating for which database do you want to get the abundance profile. Valid options are "KEGG", "PFAM" or "INTERPRO".
profile	a logical value indicating if you want to print a profile or not. This option is valid for "PFAM" and "INTERPRO" database.

Details

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

Examples

## Not run: 
read_interpro(data_interpro="inst/extdata/Interpro_test.tsv", database="INTERPRO", 
profile = F)

## End(Not run)

mirnavazquez/RbiMs documentation built on Nov. 20, 2024, 1:16 a.m.