dada2_assign: Assign sequences using dada2 wang assigner
In vaulot/dvutils: A set of utilities
Description
Usage
Arguments
Value
Description
Write out 2 files with the taxonomy and the bootstrap values. Extnesions are .dada2.taxo and .dada2.boot
The reference file should be a fasta fiel with taxonomy separated by ";"Level1;Level2;Level3;Level4;Level5;Level6;
ACCTAGAAAGTCGTAGATCGAAGTTGAAGCATCGCCCGATGATCGTCTGAAGC
Usage
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dada2_assign(
seq_file_name,
ref_file_name = "C:/daniel.vaulot@gmail.com/Databases/_PR2/versions/4.12.0/pr2_version_4.12.0_18S_dada2.fasta.gz",
tax_levels = c("kingdom", "supergroup", "division", "class", "order", "family",
"genus", "species")
)
Arguments
seq_file_name
Name of the file to assign
ref_file_name
Name of the reference sequence file. By default the latest PR2 database
tax_levels
Vector with the taxa levels
Value
A data frame with the sequence names, the assignements and the bootstrap values
vaulot/dvutils documentation built on Nov. 20, 2021, 11:01 a.m.
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Description Usage Arguments Value
Description
Write out 2 files with the taxonomy and the bootstrap values. Extnesions are .dada2.taxo and .dada2.boot
The reference file should be a fasta fiel with taxonomy separated by ";"Level1;Level2;Level3;Level4;Level5;Level6;
ACCTAGAAAGTCGTAGATCGAAGTTGAAGCATCGCCCGATGATCGTCTGAAGC
Usage
1 2 3 4 5 6 7 | dada2_assign(
seq_file_name,
ref_file_name = "C:/daniel.vaulot@gmail.com/Databases/_PR2/versions/4.12.0/pr2_version_4.12.0_18S_dada2.fasta.gz",
tax_levels = c("kingdom", "supergroup", "division", "class", "order", "family",
"genus", "species")
)
|
Arguments
seq_file_name |
Name of the file to assign |
ref_file_name |
Name of the reference sequence file. By default the latest PR2 database |
tax_levels |
Vector with the taxa levels |
Value
A data frame with the sequence names, the assignements and the bootstrap values
R Package Documentation
Browse R Packages
We want your feedback!
Note that we can't provide technical support on individual packages. You should contact the package authors for that.
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