Description Usage Arguments Details Examples
Utils to manipulate sequences or OTUs, such as extract OTUs given the subset of OTU names. They are depended on Bioconductor packages http://www.bioconductor.org/.
1 2 3 4 5 6 7 8 9 10 | subsetSequences(in.file, out.file, otus.names = c(),
regex1 = "(\\|[0-9]+)", regex2 = "", ignore.case = TRUE,
max.seq = 0)
renameFastaID(fasta, regex1 = NA, regex2 = "", ignore.case = TRUE)
rmDuplicateSeq(in.file, out.file = "unique-alg.fasta")
getTaxaMap(in.file, trait.name = "taxon", trait.value = "Bacteria",
regex1 = NA, regex2 = "", ignore.case = TRUE)
|
in.file |
The fasta file of OTU representive sequences.
Read by |
out.file |
The output fasta file containing extrated sequences. |
otus.names |
The vector of names to match sequence labels in |
regex1, regex2 |
Use for |
ignore.case |
Refer to |
max.seq |
Give the number ( |
fasta |
The fasta object returned by |
trait.name, trait.value |
The trait to annotate a tree. Its format in the string will look like '[trait.name=trait.value]'. |
subsetSequences
returns the subset of OTUs matching given OTU names.
It is depended on ShortRead
package. Follow the instruction
https://bioconductor.org/packages/release/bioc/html/ShortRead.html to install.
renameFastaID
renames the sequences id loaded from a fasta file
using ShortRead
package.
rmDuplicateSeq
removes duplicate sequences or alginments.
getTaxaMap
returns a data frame of mapping file to annotate a tree,
such as annotateRAXMLTree
.
1 2 3 4 5 6 7 | subsetSequences(in.file, otus.names, out.file)
fasta <- renameFastaID(fasta)
rmDuplicateSeq("alg.fasta", "unique-alg.fasta")
taxa.map <- getTaxaMap("16s-otus-Bacteria.fasta", trait.name="taxon", trait.value="Bacteria")
|
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