View source: R/phyloscan.fun.private.R
phsc.read.subtrees | R Documentation |
This function reads the subtree information that is generated with the phyloscanner toolkit.
phsc.read.subtrees(
prefix.infiles,
prefix.run = "ptyr",
regexpr.subtrees = "Subtrees_r_.*\\.rda$",
prefix.wfrom = "Window_",
prefix.wto = "Window_[0-9]+_to_",
save.file = NA,
resume = FALSE,
zip = FALSE
)
prefix.infiles |
Full path name that identifies subtree files |
prefix.run |
Character string to identify separate phyloscanner runs. After the prefix, an integer number is expected. For example, if prefix.run='ptyr', then files are expected to start like 'ptyr123_'. |
regexpr.subtrees |
Regular expression that identifies subtree files in the directory. By default, this is 'Subtrees_r_.*\.rda$' 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. |
data.table with columns PTY_RUN W_FROM W_TO orig.patients patient.splits tip.names.
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