link_dam_metadata: Link DAM2 or DAM5 metadata to result files

In rethomics/damr: Interface to Drosophila Activity Monitor System Result Files

Link DAM2 or DAM5 metadata to result files

Description

This function checks and add columns to DAMS metadata. This way, it can subsequently be loaded (via load_dam).

Usage

link_dam_metadata(x, result_dir)

Arguments

x	object such as a data.frame, or the name of a file (see detail)
result_dir	the root directory where all daily data are saved

Details

These function will augment metadata from two different types of inputs:

1. A data.frame (recommended) In this case, the function will try to match requested data with data available on result_dir. The provided data.frame or data.table has typically one row per requested individual and the columns (not necessarily in this order):

   • file – the name of a data file (e.g. "Monitor3.txt"), it has to exists in result_dir.

   • start_datetime – the first day and time of the requested experiment (e.g. "2014-12-28 18:00:00").

   • stop_datetime – the last day and time of the requested experiment (e.g. "2014-12-30 19:00:00" or simply "2014-12-30").

   • region_id – the channel (between 1 and 32) in which the animal was in (e.g. 20). region_id is optional. If not provided, all 32 channels are loaded with the same conditions.

   • ⁠???⁠ any number of arbitrary columns to associate conditions/treatments/genotypes/... to the previous columns.

2. The name of a CSV file that contains a table as described in 1.

The time in data is expressed relatively to start_date. In other words, if you do circadian analysis, and your D -> L transitions are at 09:00:00, you want to set start_datetime = "YYY-MM-DD 09:00:00". The ⁠result_directory`` is the folder conraining all result (.txt) files (for instance, ⁠result_dir = "C:/where/I/Store/my/txt/files/"')

Value

a data.table::data.table with the same rows as x, and extra columns used for further data loading

References

• the rethomics workflow – on the concept of "linking"

• metadata tutorial – how to work with metadata

See Also

• load_dam – to subsequently load the actual data

rethomics/damr documentation built on April 12, 2024, 12:29 p.m.