View source: R/phyloscan.fun.private.R
phsc.read.likelytransmissions | R Documentation |
This function reads likely transmissions summary files from the phyloscanner toolkit.
phsc.read.likelytransmissions(
prefix.infiles,
prefix.run = "ptyr",
regexpr.lklsu = "trmStats.csv$",
save.file = NA,
resume = FALSE,
zip = FALSE
)
prefix.infiles |
Full path name identifying likely transmissions summary 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.lklsu |
Regular expression that identifies likely transmissions summary files in the directory. |
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 trees stored in save.file. |
Data table with columns PAIR_ID, ID1, ID2, TYPE, WIN_OF_TYPE, PTY_RUN, WIN_TOTAL, SCORE
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