Reads a table object created with the read_ko function and maps each KO to the KEGG database.
mapping_ko(tibble_ko=NULL, tibble_interpro=NULL)a data frame object with four columns containing the KO abundance for each bin. Output of read_ko.
a data frame with three columns. The first column refers to contigs. They are expected to indicate in their names the bin name follow by the scaffold name divided by an "_": bin_scaffoldXX. The second column is the KEGG pathway to which such scaffold belong, and the third is the enzymes. Output of read_interpro.
This function is part of a package used for the analysis of bins metabolism.
mapping_ko(ko_bin_table)
#> # A tibble: 10,250 × 19
#> Module Module_description Pathway Pathway_description Cycle Pathway_cycle
#> <chr> <chr> <chr> <chr> <chr> <chr>
#> 1 NA NA NA NA NA NA
#> 2 NA NA map005… Glycerophospholipi… NA NA
#> 3 M00004 Pentose phosphate pat… map000… Pentose phosphate … NA NA
#> 4 M00007 Pentose phosphate pat… map000… Pentose phosphate … NA NA
#> 5 M00004 Pentose phosphate pat… map007… Carbon fixation by… NA NA
#> 6 M00007 Pentose phosphate pat… map007… Carbon fixation by… NA NA
#> 7 M00004 Pentose phosphate pat… map011… Metabolic pathways NA NA
#> 8 M00007 Pentose phosphate pat… map011… Metabolic pathways NA NA
#> 9 M00004 Pentose phosphate pat… map011… Biosynthesis of se… NA NA
#> 10 M00007 Pentose phosphate pat… map011… Biosynthesis of se… NA NA
#> # ℹ 10,240 more rows
#> # ℹ 13 more variables: Detail_cycle <chr>, Genes <chr>, Gene_description <chr>,
#> # Enzyme <chr>, KO <chr>, rbims_pathway <chr>, rbims_sub_pathway <chr>,
#> # Bin_10 <int>, Bin_12 <int>, Bin_56 <int>, Bin_113 <int>, Bin_1 <int>,
#> # Bin_2 <int>