phsc.read.processed.phyloscanner.output.in.directory: Read processed phyloscanner output

In olli0601/Phyloscanner.R.utilities:

Read processed phyloscanner output

Description

This function creates R data.tables from processed phyloscanner output, for further data analysis in R.

Usage

phsc.read.processed.phyloscanner.output.in.directory(
  prefix.infiles,
  save.file.base,
  read.likelytransmissions = TRUE,
  read.trees = TRUE,
  read.subtrees = TRUE,
  resume = FALSE,
  zip = FALSE
)

Arguments

prefix.infiles	Full path name to processed phyloscanner output
save.file.base	Output will be stored to files that start with 'save.file.base'.
read.likelytransmissions	If TRUE, read and process likely transmissions
read.trees	If TRUE, read and process trees
read.subtrees	If TRUE, read and process subtree files
resume	If TRUE, the function does not process existing rda files.
zip	If TRUE, the function zips processed phyloscanner output, and then deletes the zipped, processed phyloscanner output files.

Value

Nothing, rda objects written to file.

olli0601/Phyloscanner.R.utilities documentation built on April 26, 2024, 11:29 a.m.