TODO.md

In raim/platexpress: Inspection and Analysis of Microbial Growth and Gene Expression Data

TODO - platexpress

201812

• extend readSimplePlate to read output of writeData
• use groupStats in viewGroups
• use layout info in viewPlate; eg. plot group2

LIBRARY

fix example data to reflect current use

DATA HANDLING

readPlateData

see https://www.r-bloggers.com/a-simple-example-of-using-replyrgapply/ for approaches to the "split-apply-combine" process

high-level wrapper readPlate, where params are passed as lists,

blank correction, base adjustment, colors, IDs, and perhaps fits are all done automatically; perhaps even groupings

use classes "plate", "platedata" and "platemap" and redirect

plot.plate to viewPlate and viewGroups depending on argument groups and groups2

handle multiple plates!? see cellGrowth

-> additional plate column in plate layout -> function: mergePlates

default data IDs and colors for defined plates

order group by "by"

DATA PLOTTING

DATA PROCESSING

set above 0, after blanking

add smoothing

stats over replicates

local fits: linear, lin-expo

fit growth models: interface to grofit

1. wrapper: write more handy wrapper for grofit
2. growthrater: add wrapper for growthrater
3. findLag: find the lag and automatically subtract it using shiftData
4. addModels: add model parameters to main data structure and use in viewPlate and viewGroups

use groupStats in viewGroups

add interfaces to growthrater and cellGrowth

add function alignLag, using grofit to find lags, and subtracting

difference to the longest lag

add function fitData, where OD is fitted by grofit and all others by

cellGrowth; and fitted data are added as data$OD$fit and model parameters added

add dynamic models, eg. growthrates and BGFit

Other Packages

The bioconductor cellGrowth features non-parametric models and automatic bandwith selection.

growthrate: https://cran.r-project.org/web/packages/growthrate/index.html

OmniLog to record respiration https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3334903/

https://www.bioconductor.org/packages/release/bioc/html/cellGrowth.html

BGFit http://bmcbioinformatics.biomedcentral.com/articles/10.1186/1471-2105-14-283

GRmetrics: https://bioconductor.org/packages/devel/bioc/vignettes/GRmetrics/inst/doc/GRmetrics-vignette.html

raim/platexpress documentation built on Jan. 18, 2022, 1:41 p.m.