import_dada2 {MicrobiotaProcess} | R Documentation |
the function can import the ouput of dada2, and generated the phyloseq obj contained the argument class.
import_dada2( seqtab, taxatab = NULL, reftree = NULL, sampleda = NULL, btree = FALSE, ... )
seqtab |
matrix, feature table, the output of |
taxatab |
matrix, a taxonomic table, the output of |
reftree |
phylo or character, the phylo class of tree, or the tree file. |
sampleda |
data.frame or character, the data.frame of sample information, or the file of sample information, nrow samples X ncol factors. |
btree |
logical, whether building the tree, default is FALSE. |
..., |
additional parameters, see also |
phyloseq class contained the argument class.
Shuangbin Xu
seqtabfile <- system.file("extdata", "seqtab.nochim.rds", package="MicrobiotaProcess") taxafile <- system.file("extdata", "taxa_tab.rds", package="MicrobiotaProcess") seqtab <- readRDS(seqtabfile) taxa <- readRDS(taxafile) sampleda <- system.file("extdata", "mouse.time.dada2.txt", package="MicrobiotaProcess") ps <- import_dada2(seqtab=seqtab, taxatab=taxa, sampleda=sampleda) ps