Query regarding phyloseq object construct with QIIME output
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abhisek001 • 0
@6d5973d2
Last seen 10 weeks ago
India

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)
phyloseq microbiome Metagenomics • 247 views
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Thanks for sharing the code geometry dash

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