In npjc/readyg: Read, Validate, Simulate and Write YeastGrower Files

knitr::opts_chunk$set(
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  fig.path = "man/figures/README-",
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Read, ~~Validate~~, ~~Simulate~~ and ~~Write~~ YeastGrower (aka ACCESS) files.

Installation

# install.packages("readyg") # not yet.
remotes::install_github("npjc/readyg")

Example

Yeast Grower/ACCESS files are written in windows ini format (sort-of). read_yg() parses this format and returns the data in a format suitable for analysis or exporting (writing) to a .csv files.

library(readyg)
files <- yg_example_files()
read_yg(files[1])
read_yg(files[1], all_fields = TRUE) # full yg has quite a lot of fields...

In the individual sections:

d <- read_yg(files[1], all_fields = TRUE)
d$data
d$run_params
d$drug_data

If you want the information in the other sections , you can use read_ini() instead. This parses the ini file into a list:

l <- read_ini(files[1])
str(l, 1)

Additional Info

YeastGrower/ACCESS encodes data in non-standard ways that read_yg() corrects:

data section:

• the temperature field may be written as 300, 30, 30.0 to indicate 30ºC.
• the datetime field in the data may be written as D0_12:11:10, D0 _12:11:10 or 12:11:10 to indicate 12:11:10 on the first day of the run. To indicate what date D0 is you can provide this as an argument to e.g. read_yg('path/to/file.txt', start_date = 'YYYY-MM-DD').
  • N.B. if the datetime field is encoded as 12:11:10 and the run last longer that one day the current results may be erroneous. e.g. 12:11:10, ... , 23:48:17, ... , 00:12:34 would be encoded as the same day. This is the safe default but will provide an option to 'fix' this in the future.
• well field: The well field is encoded in row-major order ('standard') for 6,24,96, and 384 well plates but ACCESS uses a custom ordering for 48 well plates. Currently, we remap these to the standard arangement so that the wells names of a 48-well plate follow the standard convention.
  • N.B. the drug_data section, if present, can contain a Well_Alias field which is currently not checked for this inconsistency. Handle with care if using this information.

all the keys

The Yeast Grower format has some use of nearly 3000 separte keys (fields). To retrieve all of them:

yg_section_keys()

npjc/readyg documentation built on Oct. 21, 2019, 4:59 p.m.