read_ko calculates the abundance of each KO within the bins based on the KofamScan or KofamKoala output.
read_ko(data_kofam=NULL, data_kaas=NULL, data_interpro=NULL,
write=FALSE)a path where KofamScan/KofamKoala output data are. They should have the extension .txt and all files in the path are the ones that need to be read. Output data should have 5 columns with the bin names followed by the scaffold name divided by a '-' or '_': bin_scaffoldXX.
a data frame with 2 columns. Contigs are expected to indicate in their names the bin name followed by the scaffold name divided by a '-' or '_': bin_scaffoldXX.
a data frame output of read_interpro. This argument is used within mapping_ko.
a logical value indicating to save the data imported as a formatted table with .tsv extension with a time stamp and it will be located in your current working directory
This function is part of a package used for the analysis of bins metabolism.
kofam_dir <- system.file("extdata", package = "rbims")
read_ko(data_kofam = kofam_dir, write = FALSE)
#> # A tibble: 1,800 × 4
#> Scaffold_name Bin_name KO Abundance
#> <chr> <chr> <chr> <int>
#> 1 Bin_10_scaffold_10_c1_10 Bin_10 K09800 1
#> 2 Bin_10_scaffold_10_c1_100 Bin_10 K01126 2
#> 3 Bin_10_scaffold_10_c1_103 Bin_10 K00616 1
#> 4 Bin_10_scaffold_10_c1_104 Bin_10 K05539 1
#> 5 Bin_10_scaffold_10_c1_107 Bin_10 K13936 1
#> 6 Bin_10_scaffold_10_c1_109 Bin_10 K01885 1
#> 7 Bin_10_scaffold_10_c1_11 Bin_10 K09807 1
#> 8 Bin_10_scaffold_10_c1_110 Bin_10 K01737 2
#> 9 Bin_10_scaffold_10_c1_111 Bin_10 K07141 1
#> 10 Bin_10_scaffold_10_c1_116 Bin_10 K06972 1
#> # ℹ 1,790 more rows