qfaBayes: Tools for modelling the growth dynamics of arrays of large numbers of colonies and performing quantitative fitness analysis (QFA).

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A set of tools and workflows for modelling the growth dynamics of colonies arrayed on plates, as well as performing quantitative fitness analysis (QFA) on distinct (usually genetically) types of colonies. Frequent colony growth observations are required in a specific R data.frame format. qfa can use image logs generated by Colonyzer (http://research.ncl.ac.uk/colonyzer/). You can pre-process these data with our Robot Object Database (ROD: http://sourceforge.net/projects/robotobjectdb/). The model is fit either using maximum likelihood (fast), or using a hierarchical Bayesian model for all of the colonies in an experimental unit (CPU intensive). The Bayesian fit is performed using Gibbs Sampling, implemented in C. With appropriately designed experiments, qfa can also estimate genetic interaction strengths and produce epistasis plots.

Author
Jonathan Heydari <j.j.heydari@ncl.ac.uk>, with contributions from Conor Lawless <conor.lawless@ncl.ac.uk> and Darren Wilkinson <d.j.wilkinson@ncl.ac.uk>
Date of publication
2016-01-06 16:09:07
Maintainer
Conor Lawless <conor.lawless@ncl.ac.uk>
License
Artistic-2.0
Version
0.0-1
URLs

View on R-Forge

Man pages

cdc13_1_Raw_extratrim_15
cdc13_1_Raw_extratrim_15
funcARRAYTRANS
Creates and transposes an array
funcARRAYTRANS_J
Creates and transposes an array (JHM)
funcColORF
Adds NA values at the end of an ORF to give consistent Col...
funcIDorder
Order by ORF and ID coloumn
funcNoORF
Gives number of repeats for each ORF
funcNoSum
Gives running total for the number of repeats for each ORF
funcREMOVE
Filter by Screen Name, Temprature and Master Plate Number
funcRowRep
Adds NA values at the end of a repeat to give consistent row...
funcSCALING
Scales data by maximum theroetical value for IOD
funcXY
Sorts data into array with correct dimensions
funcXY_J
Sorts data into array with correct dimensions (JHM)
IHM_main
Runs IHM C code
IHM_MDRxMDP_postpro
Performs post processing for IHM
JHM_main
Runs JHM C code
JHM_postpro
Performs post processing for JHM
plot_IHM_simple
plot IHM_simple_C output
plot_JHM_simple
plot JHM_simple_C output
plot_SHM_simple
plot SHM_simple_C output
priors_IHM
priors_IHM
priors_JHM
priors_JHM
priors_SHM
priors_SHM
qfa.variables
Gives experimental variables from QFA data (colonyzer.read...
SHM_main
Runs SHM C code
SHM_postpro
Performs post processing for SHM
tuning_IHM
tuning_IHM
tuning_JHM
tuning_JHM
tuning_SHM
tuning_SHM
URA3_Raw_extratrim_15
URA3_Raw_extratrim_15
visual_convergence_simple_check_IHM
Gives a trace plot for one of every parameter type to check...
visual_convergence_simple_check_JHM
Gives a trace plot for one of every parameter type to check...
visual_convergence_simple_check_SHM
Gives a trace plot for one of every parameter type to check...

Files in this package

qfaBayes/DESCRIPTION
qfaBayes/NAMESPACE
qfaBayes/R
qfaBayes/R/functions.r
qfaBayes/R/simplifying_functions.r
qfaBayes/data
qfaBayes/data/URA3_Raw_extratrim_15.RData
qfaBayes/data/cdc13_1_Raw_extratrim_15.RData
qfaBayes/data/datalist
qfaBayes/data/priors_IHM.RData
qfaBayes/data/priors_JHM.RData
qfaBayes/data/priors_SHM.RData
qfaBayes/data/tuning_IHM.RData
qfaBayes/data/tuning_JHM.RData
qfaBayes/data/tuning_SHM.RData
qfaBayes/demo
qfaBayes/demo/00Index
qfaBayes/demo/IHM.r
qfaBayes/demo/IHM_parallel.r
qfaBayes/demo/JHM.r
qfaBayes/demo/SHM.r
qfaBayes/man
qfaBayes/man/IHM_MDRxMDP_postpro.Rd
qfaBayes/man/IHM_main.Rd
qfaBayes/man/JHM_main.Rd
qfaBayes/man/JHM_postpro.Rd
qfaBayes/man/SHM_main.Rd
qfaBayes/man/SHM_postpro.Rd
qfaBayes/man/URA3_Raw_extratrim_15.Rd
qfaBayes/man/cdc13_1_Raw_extratrim_15.Rd
qfaBayes/man/funcARRAYTRANS.Rd
qfaBayes/man/funcARRAYTRANS_J.Rd
qfaBayes/man/funcColORF.Rd
qfaBayes/man/funcIDorder.Rd
qfaBayes/man/funcNoORF.Rd
qfaBayes/man/funcNoSum.Rd
qfaBayes/man/funcREMOVE.Rd
qfaBayes/man/funcRowRep.Rd
qfaBayes/man/funcSCALING.Rd
qfaBayes/man/funcXY.Rd
qfaBayes/man/funcXY_J.Rd
qfaBayes/man/plot_IHM_simple.Rd
qfaBayes/man/plot_JHM_simple.Rd
qfaBayes/man/plot_SHM_simple.Rd
qfaBayes/man/priors_IHM.Rd
qfaBayes/man/priors_JHM.Rd
qfaBayes/man/priors_SHM.Rd
qfaBayes/man/qfa.variables.Rd
qfaBayes/man/tuning_IHM.Rd
qfaBayes/man/tuning_JHM.Rd
qfaBayes/man/tuning_SHM.Rd
qfaBayes/man/visual_convergence_simple_check_IHM.Rd
qfaBayes/man/visual_convergence_simple_check_JHM.Rd
qfaBayes/man/visual_convergence_simple_check_SHM.Rd
qfaBayes/src
qfaBayes/src/datain_IHM.c
qfaBayes/src/datain_IHM.h
qfaBayes/src/datain_JHM.c
qfaBayes/src/datain_JHM.h
qfaBayes/src/datain_SHM.c
qfaBayes/src/datain_SHM.h
qfaBayes/src/functions_IHM.c
qfaBayes/src/functions_IHM.h
qfaBayes/src/functions_JHM.c
qfaBayes/src/functions_JHM.h
qfaBayes/src/functions_SHM.c
qfaBayes/src/functions_SHM.h
qfaBayes/src/headers_IHM.h
qfaBayes/src/headers_JHM.h
qfaBayes/src/headers_SHM.h
qfaBayes/src/main_IHM.c
qfaBayes/src/main_JHM.c
qfaBayes/src/main_SHM.c
qfaBayes/src/print_IHM.c
qfaBayes/src/print_IHM.h
qfaBayes/src/print_JHM.c
qfaBayes/src/print_JHM.h
qfaBayes/src/print_SHM.c
qfaBayes/src/print_SHM.h
qfaBayes/vignettes
qfaBayes/vignettes/qfaBayes.Snw_ARCHIVE