link_ethoscope_metadata_remote {scopr} | R Documentation |
Link ethoscope metadata to the matching result files
Description
These functions augment metadata so it can be subsequently loaded (with load_ethoscope).
Usage
link_ethoscope_metadata_remote(
x,
remote_dir,
result_dir,
index_file = "index.txt",
overwrite_local = FALSE,
verbose = TRUE
)
link_ethoscope_metadata(x, result_dir = NULL, index_file = NULL)
Arguments
x |
object such as a data.frame, or the name of a file (see detail) |
remote_dir |
the url of the result directory on the data server |
result_dir |
the directory where all data are saved |
index_file |
the name of an index_file, in |
overwrite_local |
whether to download all files.
The default, |
verbose |
whether to print progress (a logical) |
Details
These function will augment metadata from two different types of inputs (x
):
A data.frame (recomended) In this case, the function will try to match requested data with data available on
result_dir
. The provided data.table::data.table has typically one row per requested individual and the columns (not necessarily in this order):-
machine_name
– the name of the machine in which the individual was (e.g."ETHOSCOPE_001"
) -
date
– the start date of the experiment formatted as"YYYY-MM-DD"
-
region_id
– the ROI in which the animal was. When not provided, all regions are queried. -
time
– the start time of the experiment formatted as "HH:MM:SS". When not provided, and multiple experiment for the same machine exist, only the last one is loaded. -
???
– any number of arbitrary columns* to associateconditions
/treatments
/genotypes
/... to the previous columns.
-
The name of a CSV file that contains a table as described in
1
.A vector of
.db
files to be read.
Value
a data.table::data.table with the same rows as x, and extra columns for further data loading
References
-
metadata tutorial – how to work with metadata
See Also
-
load_ethoscope – to load the actual data
-
list_result_files – to list available file
Examples
# Metadata with no region_id -> all regions will be loaded with the same metadata
dir <- paste0(scopr_example_dir(), "/ethoscope_results/")
data(no_region_id_metadata)
metadata <- link_ethoscope_metadata(no_region_id_metadata, dir)
print(metadata)
# Metadata with region_id -> only stated regions will be loaded with specific metadata
data(region_id_metadata)
metadata <- link_ethoscope_metadata(region_id_metadata, dir)
print(metadata)
## Not run:
# If your files are stored on a remote server,
# this will download to a local directory only the needed files
REMOTE <- "ftp://a/remote/server/"
LOCAL_DIR <- "/where/I/store/the/data/"
metadata <- link_ethoscope_metadata_remote(region_id_metadata,
REMOTE,
LOCAL_DIR)
## End(Not run)