In mirnavazquez/RbiMs: R Tools for Reconstruncting Bin Metabolisms

knitr::opts_chunk$set(
  collapse = TRUE,
  comment = "#>"
)

load("../data/Rbims.RData")

A common practice to annotate the genes of a new genome or reconstructed genome is to use InterProScan. Here are some functions to explore that information.

First, load the rbims package.

library(rbims)

The function to use that information is read_interpro. This function can parse the information of the PFAM, INTERPRO, and KEGG ids. The KEGG analysis is just possible if InterProScan was run with the -pa option. Two output options are also possible: a wide profile, or a long table.

• The database argument will parse the database. In this example, I will explore the PFAM output.

• The output format is chosen with the profile argument. When profile = T, a wide output is obtained.

• The write argument saves the formatted table generated in .tsv extension. When write = F gives you the output but not saves the table in your current directory.

If you want to follow the example you can download the use rbims test file.

interpro_pfam_profile<-read_interpro(data_interpro = "../inst/extdata/Interpro_test.tsv", database="Pfam", profile =T)

head(interpro_pfam_profile)

Or print a long table profile = F.

interpro_pfam_long<-read_interpro("../inst/extdata/Interpro_test.tsv", database="Pfam", profile = F)

head(interpro_pfam_long)

You can export this to a table like this:

write.table(interpro_pfam_long, "Interpro.tsv", quote = F, sep = "\t", row.names = F, col.names = T)

Or setting write write = T.

mirnavazquez/RbiMs documentation built on April 17, 2025, 7:37 p.m.