Commit 47d964ac authored by Sebastien Theil's avatar Sebastien Theil
Browse files

Add documentation.

parent 0ab84680
Pipeline #33133 passed with stage
in 12 seconds
......@@ -35,6 +35,8 @@ dada2_fun(
\item{r_trunclen}{Reverse read tuncate length (only for paired end 16S)}
\item{dadapool}{option for dada function (FALSE, TRUE or "pseudo"), default is "pseudo". See ? dada.}
\item{f_primer}{Forward primer sequence (only for ITS)}
\item{r_primer}{Reverse primer sequence (only for ITS)}
......@@ -57,8 +59,6 @@ dada2_fun(
\item{orient_torrent}{Forward primer sequence to orient all reads to same strand.}
\item{pool}{option for dada function (FALSE, TRUE or "pseudo"), default is "pseudo". See ? dada.}
\item{torrent_trim}{Sequence length to trim at 3' and 5' for single end torrent data. (0 = no trim)}
}
\value{
......
......@@ -11,7 +11,7 @@ export_to_stamp_fun(data = data, output = "./stamp/", correc = FALSE)
\item{output}{Output directory}
\item{correc}{If TRUE, correct metadata to replace most common special characters (eg. é -> e), save the new file in meta_stampOK.tsv.}
\item{correc}{If TRUE, correct metadata to replace most common special characters, save the new file in meta_stampOK.tsv.}
}
\value{
Export 2 text files ready to use with STAMP.
......
......@@ -17,6 +17,8 @@ generate_phyloseq_fun(
\arguments{
\item{dada_res}{Results of dada2_fun()}
\item{tax.table}{Results of assign_taxo_fun()}
\item{tree}{Results of generate_tree_fun()}
\item{metadata}{Path of metadata file (tab separated with header)}
......@@ -26,8 +28,6 @@ generate_phyloseq_fun(
\item{verbose}{Verbose level. (1: quiet, 3: verbal)}
\item{returnval}{Boolean to return values in console or not.}
\item{taxtable}{Results of assign_taxo_fun()}
}
\value{
Return a complete phyloseq object.
......
......@@ -15,9 +15,13 @@ generate_tree_fun(
\arguments{
\item{dada_res}{Results of dada2_fun()}
\item{output}{Output directory}
\item{psobj}{Phyloseq object with sequences.}
\item{output}{Output directory.}
\item{returnval}{Boolean to return values in console or not.}
\item{verbose}{Verbosity level.}
}
\value{
Return a formatted tree object ready to use in phyloseq.
......
......@@ -4,7 +4,7 @@
\alias{idTaxa_assign}
\title{IDTAXA assign}
\usage{
idTaxa_assign(db_file, dna, asv_names, confidence)
idTaxa_assign(db_file, dna, asv_names, confidence, ncpu = NULLS)
}
\arguments{
\item{db_file}{Path to IDTAXA formatted database file.}
......@@ -14,6 +14,8 @@ idTaxa_assign(db_file, dna, asv_names, confidence)
\item{asv_names}{sequences IDs in same order.}
\item{confidence}{Bootstrap threshold 0...100}
\item{ncpu}{Number of cpu to use}
}
\value{
return taxonomic assignment of given sequences.
......
......@@ -12,6 +12,8 @@ prune_db_fun(taxtable = taxtable, seqs = "", prunedb = 10, outputDIR = "./")
\item{seqs}{path to fasta file or readDNAStringSet}
\item{prunedb}{maximum number of sequences per unique taxa.}
\item{outputDIR}{Output directory.}
}
\value{
List with taxonomy table and corresponding sequences.
......
......@@ -40,5 +40,5 @@ subset_fastx(
Output fastx files in the output directory
}
\description{
Allows subset fastq or fasta files at a given threshold. This fonction can convert fastq to fasta.
Allows subset fastq or fasta files at a given threshold. This function can convert fastq to fasta.
}
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