Internal function for parsing file paths
.parse_file_paths(
config = NULL,
project_dir = waiver(),
experiment_dir = waiver(),
data_file = waiver(),
verbose = TRUE,
...
)List of paths to important directories and files.
A list of settings, e.g. from an xml file.
(optional) Path to the project directory. familiar
checks if the directory indicated by experiment_dir and data files in
data_file are relative to the project_dir.
(recommended) Path to the directory where all
intermediate and final results produced by familiar are written to.
The experiment_dir can be a path relative to project_dir or an absolute
path.
In case no project directory is provided and the experiment directory is
not on an absolute path, a directory will be created in the temporary R
directory indicated by tempdir(). This directory is deleted after closing
the R session or once data analysis has finished. All information will be
lost afterwards. Hence, it is recommended to provide either
experiment_dir as an absolute path, or provide both project_dir and
experiment_dir.
(optional) Path to files containing data that should be
analysed. The paths can be relative to project_dir or absolute paths. An
error will be raised if the file cannot be found.
The following types of data are supported.
csv files containing column headers on the first row, and samples per
row. csv files are read using data.table::fread.
rds files that contain a data.table or data.frame object. rds
files are imported using base::readRDS.
RData files that contain a single data.table or data.frame object.
RData files are imported using base::load.
All data are expected in wide format, with sample information organised row-wise.
More than one data file can be provided. familiar will try to combine
data files based on column names and identifier columns.
Alternatively, data can be provided using the data argument. These data
are expected to be data.frame or data.table objects or paths to data
files. The latter are handled in the same way as file paths provided to
data_file.
Sets verbosity.
Unused arguments