phsc.read.subtrees: Read subtree information
In olli0601/Phyloscanner.R.utilities:

phsc.read.subtrees

R Documentation

Read subtree information

Description

This function reads the subtree information that is generated with the phyloscanner toolkit.

Usage

phsc.read.subtrees(
  prefix.infiles,
  prefix.run = "ptyr",
  regexpr.subtrees = "Subtrees_r_.*\\.rda$",
  prefix.wfrom = "Window_",
  prefix.wto = "Window_[0-9]+_to_",
  save.file = NA,
  resume = FALSE,
  zip = FALSE
)

Arguments

`prefix.infiles`	Full path name that identifies subtree files
`prefix.run`	Character string to identify separate phyloscanner runs. After the prefix, an integer number is expected. For example, if prefix.run='ptyr', then files are expected to start like 'ptyr123_'.
`regexpr.subtrees`	Regular expression that identifies subtree files in the directory. By default, this is 'Subtrees_r_.\.rda$' or 'Subtrees_c_.\.rda$' from the phyloscanner toolkit.
`prefix.wfrom`	Character string to identify the start of a short read window. After the prefix, an integer number is expected. For example, if prefix.wfrom='Window_', then 'Window_800_to_1100' has start coordinate 800.
`prefix.wto`	Character string to identify the end of a short read window. After the prefix, an integer number is expected. For example, if prefix.wto='Window_[0-9]+_to_', then 'Window_800_to_1100' has end coordinate 1100.
`save.file`	If not missing, function output (a data.table) will be stored to 'save.file', input files will be zipped, and input files will be deleted.
`resume`	If TRUE and save.file is not missing, the function loads and returns subtree info stored in save.file.
`zip`	If TRUE and save.file is not missing, the function zips and removes subtree files that match the regular expression for subtrees.