multiDimBio: Multivariate Analysis and Visualization for Biological Data

Code to support a systems biology research program from inception through publication. The methods focus on dimension reduction approaches to detect patterns in complex, multivariate experimental data and places an emphasis on informative visualizations. The goal for this project is to create a package that will evolve over time, thereby remaining relevant and reflective of current methods and techniques. As a result, we encourage suggested additions to the package, both methodological and graphical.

AuthorSamuel V. Scarpino
Date of publication2016-12-16 15:35:22
MaintainerSamuel V. Scarpino <scarpino@utexas.edu>
LicenseGPL (>= 3.0)
Version1.1.1

View on CRAN

Man pages

binomPower: Power analysis for estimating the heritability of a binomial...

boxWhisker: A function to create a box and whisker plot by group ID

completeData: Function to impute missing data.

CondA: Treatment condition for animals contained in the data set...

CondB: Stress condition for animals contained in the data set Nuclei

Dyad: Housing dyad for animals contained in the data set Nuclei

FSelect: A Function to perform step-wise discriminant analysis using F...

getP: An internal function for getting empirical p values

Groups: The group ID for animals contained in the data set Nuclei

h2Estimate: Estimates the heritability of a binomial trait

IntPlot: A function to visualize the results of a MANOVA

LandscapePlot: A function to visualize the Functional Landscape of measured...

ldaPlot: A function to visualize the results of a discriminant...

Loadings: A function to visualize trait loadings onto discriminant...

makeCompMat: A function to create a pairwise comparison matrix

MeanCent: A function to scale data to mean 0

multiDimBio-package: Multivariate Analysis and Visualization for Biological Data

Nuclei: Brain activity in 14 brain regions for 71 individuals

partialF: A function to compute partial F statistics

PercentMax: A function to scale data to the percent of the maximum...

PermuteLDA: A function to determine whether two groups are in...

plotBinomPower: A function to plot the results of a binomPower run

Power: A function to estimate the error rate for FSelect and...

PPCA: A function to perform a probabilistic principle component...

Scores: Principle component scores based on the data in Nuclei

simPower: An internal function of binomPower, which actually calculates...

Functions

binomPower Man page
boxWhisker Man page
completeData Man page
CondA Man page
CondB Man page
Dyad Man page
FSelect Man page
getP Man page
Groups Man page
h2Estimate Man page
IntPlot Man page
LandscapePlot Man page
ldaPlot Man page
Loadings Man page
makeCompMat Man page
MeanCent Man page
multiDimBio Man page
multiDimBio-package Man page
Nuclei Man page
partialF Man page
PercentMax Man page
PermuteLDA Man page
plotBinomPower Man page
Power Man page
PPCA Man page
Scores Man page
simPower Man page

Files

multiDimBio
multiDimBio/inst
multiDimBio/inst/CITATION
multiDimBio/NAMESPACE
multiDimBio/data
multiDimBio/data/CondB.RData
multiDimBio/data/CondA.RData
multiDimBio/data/Nuclei.RData
multiDimBio/data/Groups.RData
multiDimBio/data/Scores.RData
multiDimBio/data/Dyad.RData
multiDimBio/R
multiDimBio/R/Loadings.R multiDimBio/R/Power.R multiDimBio/R/multiDimBio-package.R multiDimBio/R/getP.R multiDimBio/R/boxWhisker.R multiDimBio/R/simPower.R multiDimBio/R/plotBinomPower.R multiDimBio/R/h2Estimate.R multiDimBio/R/FSelect.R multiDimBio/R/MeanCent.R multiDimBio/R/makeCompMat.R multiDimBio/R/binomPower.R multiDimBio/R/PPCA.R multiDimBio/R/ZTrans.R multiDimBio/R/ldaPlot.R multiDimBio/R/partialF.R multiDimBio/R/LandscapePlot.R multiDimBio/R/completeData.R multiDimBio/R/PercentMax.R multiDimBio/R/PermuteLDA.R multiDimBio/R/IntPlot.R
multiDimBio/MD5
multiDimBio/DESCRIPTION
multiDimBio/man
multiDimBio/man/CondA.Rd multiDimBio/man/PercentMax.Rd multiDimBio/man/makeCompMat.Rd multiDimBio/man/IntPlot.Rd multiDimBio/man/Scores.Rd multiDimBio/man/Power.Rd multiDimBio/man/getP.Rd multiDimBio/man/simPower.Rd multiDimBio/man/boxWhisker.Rd multiDimBio/man/FSelect.Rd multiDimBio/man/h2Estimate.Rd multiDimBio/man/ldaPlot.Rd multiDimBio/man/PermuteLDA.Rd multiDimBio/man/Loadings.Rd multiDimBio/man/Groups.Rd multiDimBio/man/MeanCent.Rd multiDimBio/man/PPCA.Rd multiDimBio/man/partialF.Rd multiDimBio/man/Nuclei.Rd multiDimBio/man/CondB.Rd multiDimBio/man/multiDimBio-package.Rd
multiDimBio/man/ztrans.rd
multiDimBio/man/LandscapePlot.Rd multiDimBio/man/binomPower.Rd multiDimBio/man/completeData.Rd multiDimBio/man/plotBinomPower.Rd multiDimBio/man/Dyad.Rd

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.