layouts: collate layout file for a screen
In olobiolo/siscreenr: Analyze Genome-Wide siRNA Screening Campaigns

Description Usage Arguments Details Value

Take any number of layout files and create a single layout file. There must be exactly one file per plate type but each file may contain layouts for different plating dates and these may be different.

1	layouts(..., outfile = NULL)

`...`	files or a character vector of files to load and collate
`outfile`	file to save the layout in

This is a utility function for neatly putting together many layouts. Sometimes a layout changes over the course of the screen. In that case it is easy (if a little tedious) to prepare a composite layout file with a separate column for every plating date. This function will load all such files and convert them into a single file that can be loaded with build_screen. If your screen maintains the same layout throughout, running this function is redundant.

The output file is a tab delimited text file that contains a long-form table with the following columns: well, well_type, plate_type, and possibly plated.

Input files must follow these rules:

1. must be tab delimited text files with a header

2. must have a "well" column with integer well numbers

3. must have the plate type encoded either as a "plate_type" column or in the file name as the last element before the extension, e.g. "layout_S14_test.txt"

4. if there is a single layout, it must be in a column called "well_type"

5. if there is more than one layout, each must be placed in a separate column, the name of which must be the plating date in yyyymmdd format (legal separators are allowed)

There should also be a "position" column or "row" and "column" columns but this is optional.

If outfile is not specified, the collated layout table, otherwise nothing.

olobiolo/siscreenr documentation built on Nov. 26, 2021, 3:08 p.m.