I used qiime pipeline to analyze 16s amplicon sequencing data now I want to take those outputs into r studio with the help of phyloseq package and want to create phyloseq object that's how I can do downstream analysis. can anyone give a real-time example of the r command to perform the mentioned operation? I detected two commands but I was unable to use them. my other question what is the map file is looking here and refseqfilename do you have any real data-based examples of those files? Thanks.
import_qiime(otufilename = NULL, mapfilename = NULL, treefilename = NULL, refseqfilename = NULL, refseqFunction = readDNAStringSet, refseqArgs = NULL, parseFunction = parse_taxonomy_qiime, verbose = TRUE, ...) otufile <- system.file("extdata", "GP_otu_table_rand_short.txt.gz", package="phyloseq") mapfile <- system.file("extdata", "master_map.txt", package="phyloseq") trefile <- system.file("extdata", "GP_tree_rand_short.newick.gz", package="phyloseq") import_qiime(otufile, mapfile, trefile)