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.
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)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.
a character indicating for which database do you want to get the abundance profile. Valid options are "KEGG", "PFAM" or "INTERPRO".
a logical value indicating if you want to print a profile or not. This option is valid for "PFAM" and "INTERPRO" database.
This function is part of a package used for the analysis of bins metabolism.
read_interpro(data_interpro = "inst/extdata/Interpro_test.tsv",
database = "INTERPRO", profile = FALSE)
#> Error in .data$X12: Column `X12` not found in `.data`.