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)
| tibble_ko | a data frame object with four columns containing the KO abundance for each bin. Output of read_ko. |
|---|---|
| tibble_interpro | 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: 9,882 x 19 #> Module Module_description Pathway Pathway_descripti… Cycle Pathway_cycle #> <chr> <chr> <chr> <chr> <chr> <chr> #> 1 NA NA NA NA NA NA #> 2 NA NA map00564 Glycerophospholip… NA NA #> 3 M00004 Pentose phosphate pat… map00030 Pentose phosphate… NA NA #> 4 M00007 Pentose phosphate pat… map00030 Pentose phosphate… NA NA #> 5 M00004 Pentose phosphate pat… map01100 Metabolic pathways NA NA #> 6 M00007 Pentose phosphate pat… map01100 Metabolic pathways NA NA #> 7 M00004 Pentose phosphate pat… map01110 Biosynthesis of s… NA NA #> 8 M00007 Pentose phosphate pat… map01110 Biosynthesis of s… NA NA #> 9 M00004 Pentose phosphate pat… map01120 Microbial metabol… NA NA #> 10 M00007 Pentose phosphate pat… map01120 Microbial metabol… NA NA #> # … with 9,872 more rows, and 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>