In EngeLab/EngeMetadata: Handles R import of Google Drive based metadata for the Enge lab

Release build: Test coverage:

Installation

if(!"devtools" %in% rownames(installed.packages())) {
  install.packages("devtools")
}
devtools::install_github("EngeLab/EngeMetadata")

Template setup

All instructions herein are case sensitive and tense specific, i.e. "Well" is not the same as "well" and "Well" is not the same as "Wells".

The template design is based on sheet precedence with Wells > Columns > Plate. This means e.g. if a key is present in the Plate sheet and also present in Columns sheet, the values in the Columns sheet will overwrite the values in the Plate sheet where they differ.

Workbook

• Must include 3 sheets named "Plate", "Columns", and "Wells". Note that the names are plural.

Plate sheet

• Should only contain 2 columns named "Key" and "Value".
• The unique_key key is mandatory and should match the file name.
• The wells_in_plate key is mandatory. Possible values are 384 or 96. More possibilities in Adding non-standard metadata section.
• Note that if the whole plate does not contain cells, this may be annotated with the "Missing" key (in either the Columns or Wells sheet). If "Missing" is given the value TRUE, it these samples will be removed from the metadata downstream. Otherwise the whole plate, according to the wells_in_plate key, is assumed to contain cells.

Columns sheet

• The Column key is mandatory. Note that this is singular.
• The Column key values must include all columns present in the plate type given by the wells_in_plate key in the Plate sheet. Single digit columns should be prefixed with a 0, i.e. "01" not "1".

Wells sheet

• The Well key is mandatory. Note that this is singular.
• The Well key values must include all wells in the plate type given by the wells_in_plate key in the Plate sheet. Single digit columns should be prefixed with a 0, i.e. "A01" not "A1".

Dates

• Dates are expected to have the word "date" somewhere in the key.
• Dates including a month or day that is a single digit should be prefixed with a "0", i.e. "01" for January and not "1" likewise "01" for the first of the month not "1".
• Dates should be formatted year, month, day without spaces. Acceptable syntax is: 20181201 or 181201.

Importing metadata into R

There is currently only one exported function in the package which is called "metadata". The metadata function takes a plate/file name and a googledrive path as arguments and downloads, processes, and returns the metadata as a tibble. Precedence is resolved automatically and the metadata is expanded so that there is one entry per sample.

Adding non-standard metadata

There is some limited functionality for adding metadata for non-standard datasets, e.g. datasets produced by other labs that don't necessiarily conform well to the typical Enge lab setup. This can be achieved by substituting the value in the wells_in_plate key for the number of samples and, in addition, removing all columns from the Columns sheet. The current setup only allows for metadata associated with an entire experiment or individual samples (which can be annotated in the wells sheet).

EngeLab/EngeMetadata documentation built on March 23, 2021, 8:19 p.m.