qfaBayes: Tools for modelling the growth dynamics of arrays of large numbers of colonies and performing quantitative fitness analysis (QFA).
Version 0.0-1

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
URL http://qfa.r-forge.r-project.org/
Package repositoryView on R-Forge
InstallationInstall the latest version of this package by entering the following in R:
install.packages("qfaBayes", repos="http://R-Forge.R-project.org")

Popular man pages

funcREMOVE: Filter by Screen Name, Temprature and Master Plate Number
funcRowRep: Adds NA values at the end of a repeat to give consistent row...
funcXY: Sorts data into array with correct dimensions
funcXY_J: Sorts data into array with correct dimensions (JHM)
IHM_MDRxMDP_postpro: Performs post processing for IHM
plot_JHM_simple: plot JHM_simple_C output
tuning_JHM: tuning_JHM
See all...

All man pages Function index File listing

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

Files

DESCRIPTION
NAMESPACE
R
R/functions.r
R/simplifying_functions.r
data
data/URA3_Raw_extratrim_15.RData
data/cdc13_1_Raw_extratrim_15.RData
data/datalist
data/priors_IHM.RData
data/priors_JHM.RData
data/priors_SHM.RData
data/tuning_IHM.RData
data/tuning_JHM.RData
data/tuning_SHM.RData
demo
demo/00Index
demo/IHM.r
demo/IHM_parallel.r
demo/JHM.r
demo/SHM.r
man
man/IHM_MDRxMDP_postpro.Rd
man/IHM_main.Rd
man/JHM_main.Rd
man/JHM_postpro.Rd
man/SHM_main.Rd
man/SHM_postpro.Rd
man/URA3_Raw_extratrim_15.Rd
man/cdc13_1_Raw_extratrim_15.Rd
man/funcARRAYTRANS.Rd
man/funcARRAYTRANS_J.Rd
man/funcColORF.Rd
man/funcIDorder.Rd
man/funcNoORF.Rd
man/funcNoSum.Rd
man/funcREMOVE.Rd
man/funcRowRep.Rd
man/funcSCALING.Rd
man/funcXY.Rd
man/funcXY_J.Rd
man/plot_IHM_simple.Rd
man/plot_JHM_simple.Rd
man/plot_SHM_simple.Rd
man/priors_IHM.Rd
man/priors_JHM.Rd
man/priors_SHM.Rd
man/qfa.variables.Rd
man/tuning_IHM.Rd
man/tuning_JHM.Rd
man/tuning_SHM.Rd
man/visual_convergence_simple_check_IHM.Rd
man/visual_convergence_simple_check_JHM.Rd
man/visual_convergence_simple_check_SHM.Rd
src
src/datain_IHM.c
src/datain_IHM.h
src/datain_JHM.c
src/datain_JHM.h
src/datain_SHM.c
src/datain_SHM.h
src/functions_IHM.c
src/functions_IHM.h
src/functions_JHM.c
src/functions_JHM.h
src/functions_SHM.c
src/functions_SHM.h
src/headers_IHM.h
src/headers_JHM.h
src/headers_SHM.h
src/main_IHM.c
src/main_JHM.c
src/main_SHM.c
src/print_IHM.c
src/print_IHM.h
src/print_JHM.c
src/print_JHM.h
src/print_SHM.c
src/print_SHM.h
vignettes
vignettes/qfaBayes.Snw_ARCHIVE
qfaBayes documentation built on May 21, 2017, 12:14 a.m.

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