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

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.

AuthorJonathan 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 publication2016-01-06 16:09:07
MaintainerConor Lawless <conor.lawless@ncl.ac.uk>
LicenseArtistic-2.0
Version0.0-1
http://qfa.r-forge.r-project.org/

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...

Functions

cdc13_1_MPlate15only Man page
funcARRAYTRANS Man page
funcARRAYTRANS_J Man page
funcColORF Man page
funcIDORDER Man page
funcNoORF Man page
funcNoSum Man page
funcREMOVE Man page
funcRowRep Man page
funcSCALING Man page
funcXY Man page
funcXY_J Man page
IHM_main Man page
IHM_MDRxMDP_postpro Man page
JHM_main Man page
JHM_postpro Man page
plot_IHM_simple Man page
plot_JHM_simple Man page
plot_SHM_simple Man page
priors_IHM Man page
priors_JHM Man page
priors_SHM Man page
qfa.variables Man page
SHM_main Man page
SHM_postpro Man page
tuning_IHM Man page
tuning_JHM Man page
tuning_SHM Man page
URA3_MPlate15only Man page
visual_convergence_simple_check_IHM Man page
visual_convergence_simple_check_JHM Man page
visual_convergence_simple_check_SHM Man page

Files

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

Questions? Problems? Suggestions? or email at ian@mutexlabs.com.

Please suggest features or report bugs with the GitHub issue tracker.

All documentation is copyright its authors; we didn't write any of that.