GeneticTools: Collection of Genetic Data Analysis Tools
Version 0.3.1

A loose collection of tools for the analysis of gene expression and genotype data, currently with main focus on eQTL and MDR analysis.

AuthorDaniel Fischer
Date of publication2015-02-04 13:12:25
MaintainerDaniel Fischer <daniel.fischer@luke.fi>
LicenseGPL (>= 2)
Version0.3.1
Package repositoryView on CRAN
InstallationInstall the latest version of this package by entering the following in R:
install.packages("GeneticTools")

Getting started

Package overview

Popular man pages

calcDistances: Calculate Distances Between Time Series
genotData: Simulated Genotype Data
getRegionsOI: Filter Annotation File
mdr: Perform a MDR.
predict.mdr: Calculates MDR Ensemble Classifier
print.mdr: Print an mdr Object
recodeData: Recode a Genotype Data Matrix.
See all...

All man pages Function index File listing

Man pages

annotTrack: Example Annotation Track
calcDistances: Calculate Distances Between Time Series
eQTL: Perform an eQTL Analysis
GeneticTools-package: GeneticTools
genotData: Simulated Genotype Data
genotypePlot: Expression Boxplots
getRegionsOI: Filter Annotation File
gtfToBed: Extract the Chromosomal Information Required in bed Format...
mdr: Perform a MDR.
plot.eqtl: Plot an eqtl Object
plot.mdr: Plot an MDR Object
predict.mdr: Calculates MDR Ensemble Classifier
print.eqtl: Print an eqtl Object
print.mdr: Print an mdr Object
realSNPs: Simulated SNP Data
recodeData: Recode a Genotype Data Matrix.
summary.eqtl: Summarize an eqtl Object
visTrans: Visualize trans-eQTL Results
Xgene: Simulated Expression Data

Functions

R/GeneticTools-package Man page
Xgene Man page
annotTrack Man page
calcDistances Man page
eQTL Man page
genotData Man page
genotypePlot Man page
getRegionsOI Man page
gtfToBed Man page
mdr Man page
plot,eqtl-method Man page
plot,mdr-method Man page
plot-method Man page
plot.eqtl Man page
plot.mdr Man page
predict.mdr Man page
print,eqtl-method Man page
print,mdr-method Man page
print-method Man page
print.eqtl Man page
print.mdr Man page
realSNPs Man page
recodeData Man page
summary,eqtl-method Man page
summary-method Man page
summary.eqtl Man page
visTrans Man page

Files

GeneticTools
GeneticTools/inst
GeneticTools/inst/ChangeLog
GeneticTools/ToDo
GeneticTools/src
GeneticTools/src/Makevars
GeneticTools/src/mdr.h
GeneticTools/src/timeCluster.h
GeneticTools/src/mdr.cpp
GeneticTools/src/timeCluster.cpp
GeneticTools/src/Makevars.win
GeneticTools/NAMESPACE
GeneticTools/data
GeneticTools/data/annotTrack.rda
GeneticTools/data/Xgene.rda
GeneticTools/data/realSNPs.rda
GeneticTools/data/genotData.rda
GeneticTools/R
GeneticTools/R/predict.mdr.R
GeneticTools/R/mdrEnsemble.R
GeneticTools/R/visTrans.R
GeneticTools/R/getRegionsOI.R
GeneticTools/R/joinEQTLsig.R
GeneticTools/R/print.eqtl.R
GeneticTools/R/rearrange.R
GeneticTools/R/plot.eqtl.R
GeneticTools/R/QTL.R
GeneticTools/R/gtfToBed.R
GeneticTools/R/makeannotList.R
GeneticTools/R/eqtlLM.R
GeneticTools/R/mdr.R
GeneticTools/R/recodeData.R
GeneticTools/R/plotGeneLocation.R
GeneticTools/R/calcDistances.R
GeneticTools/R/getSNPlocations.R
GeneticTools/R/print.mdrPredict.R
GeneticTools/R/cWrappers.R
GeneticTools/R/columnLabels.R
GeneticTools/R/genotypePlot.R
GeneticTools/R/eqtlDir.R
GeneticTools/R/eqtl.R
GeneticTools/R/summary.eqtl.R
GeneticTools/R/joinEQTL.R
GeneticTools/R/plot.mdr.R
GeneticTools/R/print.mdr.R
GeneticTools/vignettes
GeneticTools/vignettes/GeneticTools.tex
GeneticTools/vignettes/GeneticTools.pdf
GeneticTools/MD5
GeneticTools/DESCRIPTION
GeneticTools/man
GeneticTools/man/mdr.Rd
GeneticTools/man/getRegionsOI.Rd
GeneticTools/man/Xgene.Rd
GeneticTools/man/genotypePlot.Rd
GeneticTools/man/eQTL.Rd
GeneticTools/man/calcDistances.Rd
GeneticTools/man/print.eqtl.Rd
GeneticTools/man/visTrans.Rd
GeneticTools/man/annotTrack.Rd
GeneticTools/man/plot.mdr.Rd
GeneticTools/man/GeneticTools-package.Rd
GeneticTools/man/predict.mdr.Rd
GeneticTools/man/recodeData.Rd
GeneticTools/man/summary.eqtl.Rd
GeneticTools/man/realSNPs.Rd
GeneticTools/man/plot.eqtl.Rd
GeneticTools/man/genotData.Rd
GeneticTools/man/print.mdr.Rd
GeneticTools/man/gtfToBed.Rd
GeneticTools documentation built on Jan. 15, 2017, 11:21 a.m.

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

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

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