workflow/PICRUSt.R

In xieguigang/metagenomics: Metagenomics/16S data analysis

require(GCModeller);

imports "taxonomy_kit" from "metagenomics_kit";
imports "microbiome" from "metagenomics_kit";

[@info "the mothur OTU table output results."]
[@type "filepath"]
const otu_file as string = ?"--out_table" || stop("A mothur OTU table file must be provided!");
[@info "the predicted metagenome output table file path."]
[@type "filepath"]
const outfile  as string = ?"--out_KO" || `${dirname(otu_file)}/metagenome.csv`;
[@info "the PICRUSt matrix file"]
[@type "filepath"]
const matrixKO as string = ?"--matrix" || "/opt/metagenomics/ko_13_5_precalculated.PICRUSt";

using PICRUSt as file(matrixKO) {

	OTUtable = read.csv(otu_file, row.names = "taxonomy");
	OTUtable[, "OTU_num"] = NULL;
	
	metagenome = PICRUSt
	|> read.PICRUSt_matrix()
	|> predict_metagenomes(OTUtable)
	|> as.data.frame()
	;
	
	# run enrichment analysis
	write.csv(metagenome, file = outfile, row.names = TRUE);
}