prune_paralogs_MO: Identify orthologs using the "MO" method.

In joelnitta/baitfindR: Find Baits for Sequence Capture

Description

Given a folder containing homolog trees, prune paralogs from the trees using the monophyletic outgroups (MO) method. For trees that have non-repeating, monophyletic outgroups, this method extracts the largest subtree containing the outgroup. Trees that consist solely of one-to-one orthologs (i.e., no duplications within a sample/taxon) will also be retained. This function will overwrite any output files with the same name in outdir.

Usage

prune_paralogs_MO(
  path_to_ys = pkgconfig::get_config("baitfindR::path_to_ys"),
  tree_folder,
  tree_file_ending,
  ingroup,
  outgroup,
  minimal_taxa = 4,
  outdir,
  overwrite = FALSE,
  get_hash = TRUE,
  echo = pkgconfig::get_config("baitfindR::echo", fallback = FALSE),
  ...
)

Arguments

path_to_ys	Character vector of length one; the path to the folder containing Y&S python scripts, e.g., "/Users/me/apps/phylogenomic_dataset_construction/"
tree_folder	Character vector of length one; the path to the folder containing the trees to be used for pruning.
tree_file_ending	Character vector of length one; only tree files with this file ending will be used.
ingroup	Character vector; names of ingroup taxa/samples.
outgroup	Character vector; names of outgroup taxa/samples.
minimal_taxa	Numeric; minimal number of taxa required for tree to be included. Default 4, the minimum number of taxa needed for an un-rooted tree.
outdir	Character vector of length one; the path to the folder where the pruned trees should be written.
overwrite	Logical; should previous output of this command be erased so new output can be written? Once erased it cannot be restored, so use with caution!
get_hash	Logical; should the 32-byte MD5 hash be computed for all pruned tree files concatenated together? Used for by drake_plan for tracking during workflows. If TRUE, this function will return the hash.
echo	Logical; should the standard output and error be printed to the screen?
...	Other arguments. Not used by this function, but meant to be used by drake_plan for tracking during workflows.

Details

Wrapper for Yang and Smith (2014) prune_paralogs_MO.py

Value

For each tree file ending in tree_file_ending in tree_folder, putative orthologs will be extracted from the tree using the MO method and written to outdir with the file ending .ortho.tre; re-rooted trees will also be written with the file ending .reroot. If get_hash is TRUE, the 32-byte MD5 hash be computed for all extracted tree files concatenated together will be returned.

Author(s)

Joel H Nitta, [e-mail]

References

Yang, Y. and S.A. Smith. 2014. Orthology inference in non-model organisms using transcriptomes and low-coverage genomes: improving accuracy and matrix occupancy for phylogenomics. Molecular Biology and Evolution 31:3081-3092. https://bitbucket.org/yangya/phylogenomic_dataset_construction/overview

Examples

## Not run: prune_paralogs_MO(tree_folder = "some/folder/containing/tree/files", tree_file_ending = ".tre", outgroup = c("ABC", "EFG"), ingroup = c("HIJ", "KLM"), outdir = "some/folder")

joelnitta/baitfindR documentation built on May 7, 2020, 6:21 p.m.