#' read_uparse
#'
#' uparse readin function
#'
#' read outputs from Ying's uparse pipeline into a phyloseq object
#' @param directory directory containing uparse output files (usually called 'uparse')
#' requires phyloseq, ape, yingtools2, dplyr
#' @examples phy <- read_uparse("Z:/Eric/uparse")
#' @export
read_uparse <- function(directory){
setwd(directory)
biom.file <- "total.8.otu-tax.biom"
seq.file <- "total.5.repset.fasta"
tree.file <- "total.10.tree"
tax.file <- "total.5.repset.fasta.blastn.refseq_rna.txt"
biom <- import_biom(biom.file)
seq <- import_qiime(refseqfilename=seq.file)
tree <- read.tree.uparse(tree.file)
taxa_names(tree) <- gsub("\\_\\_","\\;",taxa_names(tree))
tax <- read.blastn.file(tax.file) %>% set.tax()
phy <- merge_phyloseq(biom,seq,tree)
tax_table(phy) <- tax
rm(biom.file,seq.file,tax.file,tree.file,biom,seq,tax,tree)
return(phy)
}
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