52 lines
1.4 KiB
R
52 lines
1.4 KiB
R
% Generated by roxygen2: do not edit by hand
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% Please edit documentation in R/import.metabarcoding.R
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\name{import.metabarcoding.data}
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\alias{import.metabarcoding.data}
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\title{Read a data file produced by the \code{obitab} command}
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\usage{
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import.metabarcoding.data(file, sep = "\\t", sample = "sample",
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sample.sep = "\\\\.", attribute = ":")
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}
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\arguments{
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\item{file}{a string containing the file name of the obitab file.}
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\item{sep}{Column separator in the obitab file.
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The default separator is the tabulation.}
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\item{sample}{A regular expression allowing to identify columns
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from the file describing abundances of sequences per sample}
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\item{sample.sep}{Separator between combined sample name.}
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\item{attribute}{Separator used to split between sample 'tag' and sample name.}
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}
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\value{
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a \code{\link{metabarcoding.data}} instance
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}
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\description{
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Read a data file issued from the conversion of a \strong{fasta}
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file to a tabular file by the \code{obitab} command of the
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\strong{OBITools} package
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}
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\examples{
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require(ROBITools)
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\dontshow{# switch the working directory to the data package directory}
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\dontshow{setwd(system.file("extdata", package="ROBITools"))}
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# read the termes.tab file
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termes=import.metabarcoding.data('termes.tab')
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# print the number of samples and motus described in the file
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dim(termes)
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}
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\seealso{
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\code{\link{metabarcoding.data}}
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}
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\author{
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Eric Coissac
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}
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\keyword{DNA}
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\keyword{metabarcoding}
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